Biocatalytic process for preparing eslicarbazepine and analogs thereof

ABSTRACT

The present disclosure relates to biocatalysts and its uses for the efficient preparation of eslicarbazepine, eslicarbazepine acetate, and analogs thereof.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a national stage application filed under 35USC §371 and claims priority of the international applicationPCT/US2012/033347, filed Apr. 12, 2012, and U.S. provisional patentapplications 61/475,103, filed Apr. 13, 2011, each of which is herebyincorporated by reference herein.

1. TECHNICAL FIELD

The present disclosure relates to biocatalyst-mediated processes forproducing chiral compounds and biocatalysts used in the processes.

2. REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM

The official copy of the Sequence Listing is submitted concurrently withthe specification as an ASCII formatted text file via EFS-Web, with afile name of “CX2-085WO1_ST25.txt”, a creation date of Apr. 12, 2012,and a size of 65,605 bytes. The Sequence Listing filed via EFS-Web ispart of the specification and is hereby incorporated in its entirety byreference herein.

3. BACKGROUND

Oxcarbazepine(10-oxo-10,11-dihydro-5H-dibenzo[b,f]azepine-5-carboxamide) is a 10-ketoanalogue of carbamazepine (dibenzo[b,f]azepine-5-carboxamide). Thestructurally similar compounds

are known to block voltage-gated sodium channel activity and indicatedfor use in the treatment of epilepsy. Oxcarbazepine was designed toavoid the oxidative metabolic transformation of carbamazepine.Oxcarbazepine itself undergoes rapid conversion in vivo to a mixture of(S)-10-hydroxy-10,11-dihydro-5H-dibenzo[b,f]axepine-5-carboxamide(S-licarbazepine or eslicarbazepine) and(R)-10-hydroxy-10,11-dihydro-5H-dibenzo[b,f]azepine-5-carboxamide(R-licarbazepine)

Based on the active metabolites of oxcarbazepine, eslicarbazepineacetate, chemically known as(S)-5-carbamoyl-10,11-dihydro-5H-dibenzo[b,f]azepin-10-yl acetate(structure shown below),

was developed on the view that the S-isomer would be a morephysiologically effective, have fewer adverse effects, and cross theblood brain barrier more efficiently than R-licarbazepine.Eslicarbazepine acetate prodrug is efficiently absorbed in thegastrointestinal tract and is metabolized to eslicarbazepine byhydrolysis of the acetate group (Rauchenzauner, M. and Luef, G., 2010,Neuropsychiatr Dis Treat. 6: 723-730).

Chemical preparation of eslicarbazepine acetate is described inUS2007119197, WO02092572, WO2007117166, WO2007012793, and WO2010113179.One process involves preparing a racemic mixture, resolving the (S) and(R) enantiomers of licarbazepine from the racemic mixture and using theintermediates to form the S- and R-licarbazepine acetate. Anotherprocess involves reduction of oxcarbazepine in the presence of acatalyst and a hydride source to form S-licarbazepine in enantiomericexcess. Eslicarbazepine acetate can also be prepared directly byasymmetric hydrogenation of the enol acetate of oxcarbazepine. See,e.g., WO2007117166.

Publication IPCOM000193904D describes carbonyl reductase (ketoreductase)mediated conversion of oxcarbazepine to S- or R-licarbazepine. Theketoreductases produced either R- or S-licarbazepine in enantiomericexcess, thus indicating differences in stereoselectivity, depending onthe type of carbonyl reductase used. The reaction conditions, whichincluded a temperature of 30° C. and time of 18-24 h or a temperature of40° C. and a time of 18 to 24 h resulted in conversion of only about 6%to about 21% to product (defined as EsCBZ purity).

It is desirable to have efficient and cost-effective processes forsynthesis of eslicarbazepine and eslicarbazepine acetate, for exampleprocesses that result in conversion of >90% of starting compound toeslicarbazepine in >98% enantiomeric excess. Particularly desirable areefficient processes capable of high percent production ofeslicarbazepine with high loading of starting compound (e.g., ≧100 g/Lof oxcarbazepine).

4. SUMMARY

The present disclosure provides processes for the biocatalyticconversion of oxcarbazepine (compound (2c),10-oxo-10,11-dihydro-5H-dibenzo[b,f]azepine-5-carboxamide and structuralanalogs thereof to chiral alcohol eslicarbazepine (compound (1c),5S-5-hydroxy-5,6-dihydrobenzo[b][1]benzazepine-11-carboxamide) orcorresponding chiral alcohol analogs in enantiomeric excess, asillustrated in Scheme 1,

polypeptides that mediate the conversion, polynucleotides encoding thepolypeptides, and methods of making the polypeptides for use in theprocesses.

The biocatalysts are ketoreductases derived from Lactobacillus,particularly non-naturally occurring ketoreductases engineered formediating the conversion with increased activity, high enantiomericexcess, high percent conversion in the presence of high substrateloading, and capable of regenerating the cofactor by its in situactivity as an alcohol dehydrogenase.

Accordingly, in some embodiments, the process for preparing compound(1c) in enantiomeric excess comprises contacting compound (2c) with aketoreductase described herein, particularly a non-naturally occurringor engineered polypeptides of the present disclosure in the presence ofNADPH or NADH cofactor under suitable reaction conditions.

In another aspect, a structural analog of compound (1c) can be preparedin enantiomeric excess using the ketoreductases described herein. Insome embodiments, the structural analog are encompassed by structuralformula (1)

wherein

each ring A and B is independently an optionally substituted monocyclicaryl or heteroaryl,

R¹ is selected from hydrogen, hydroxy, halo, cyano, carboxy, and anoptionally substituted alkyl, aminoalkyl, cycloalkyl, heterocycloalkyl,alkyloxycarbonyl, aminocarbonyl, aminothiocarbonyl, aminosulfonyl, andsulfonyl. In some embodiments, R¹ is selected from H, —OH, —CN,—C(O)OR^(a), —(C1-C4)alkyl-NR^(b)R^(c), —C(O)NR^(b)R^(c),—C(S)NR^(b)R^(c), —SO₂NR^(b)R^(c), —SO₂R^(b), bicycloalkyl andheterobicycloalkyl, wherein R^(a), R^(b) and R^(c) are eachindependently selected from H and an optionally substituted alkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl. Insome embodiments, R¹ is —C(O)NH₂, dimethylaminopropyl,methylaminopropyl, and quinuclidinyl. Other chiral alcohol compounds ofstructural formula (1) that can be prepared are further described in thedetailed description.

In some embodiments, the method for preparing a compound of structuralformula (1) comprises contacting a compound of structural formula (2)

wherein rings A and B, and R¹ are defined above, with any of theketoreductases of the present disclosure, in presence of NADH or NADPHunder suitable reaction conditions.

Suitable reactions conditions for the conversion of compound (2c) tocompound (1c) and compounds of structural formula (2) to compounds ofstructural formula (1) in enantiomeric excess employing ketoreductasesare provided in greater detail in the description below, including butnot limited to ranges of pH, temperature, buffer, solvent system,substrate loading, polypeptide loading, cofactor loading, and reactiontime.

In some embodiments, the improvements in enzyme properties of thenon-natural, engineered ketoreductases allow the process to be carriedout in, by way of example, a pH range of about 6 to about 12, atemperature of about 20° C. to about 60° C., and a NADPH or NADHcofactor concentration of about 0.03 g/L to about 1 g/L. The engineeredpolypeptides with improved enzyme properties can be used at lowerconcentrations to reduce the amount of protein residue that must beremoved in subsequent workup of the product, and can vary, by way ofexample and not limitation, from 0.1 g/L to about 10 g/L, about 0.1 g/Lto about 5 g/L, about 0.1 g/L to about 2 g/L, or about 0.1 g/L to about1.0 g/L. The substrate loading, particularly with reference to compound(2c) can be from, by way of example, from about 1 g/L to 100 g/L orgreater. In some embodiments, the process can be carried out, whereinthe engineered ketoreductase is immobilized on a solid support.

In some embodiments, the process for preparing compound (1c) orcompounds of structural formula (1) can further comprise a cofactorregeneration system capable of converting NADP+ to NADPH, or NAD⁺ toNADH. A cofactor recycling system can enhance the efficiency ofconversion while lowering the amount of cofactor required in thereaction. The cofactor recycling system comprises a dehydrogenase and acorresponding substrate, for example, glucose dehydrogenase and glucose,glucose phosphate dehydrogenase and glucose-6-phosphate, formatedehydrogenase and formate, and a ketoreductase/alcohol dehydrogenase anda secondary alcohol, e.g., isopropanol (IPA). In some embodiments, theketoreductases capable of converting compound (2c) to compound (1c) isalso capable of acting as a cofactor recycling system by converting asecondary alcohol, for example isopropanol, to its corresponding ketone.Accordingly, a secondary alcohol, particularly isopropanol, can be usedin a co-solvent system in the process with the engineered ketoreductasesof the disclosure to convert compound (2c) or compounds of structuralformula (2) to compound (2c) or compounds of structural formula (1),respectively, and also regenerate the cofactor, particularly NADPH,using IPA as the substrate.

In some embodiments, the processes can be used to convert at least about91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater of compound (2c)to compound (1c) in 24 h or less.

In some embodiments, the process can be used to convert compound (2c) tocompound (1c) enantiomeric excess of at least about 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99% or greater of compound (1c) in 24 h or less.

In the embodiments herein, the ketoreductases for use in the process arederived from Lactobacillus, particularly Lactobacillus kefir. In someembodiments, the ketoreductases are non-natural, engineeredketoreductases that have residue differences as compared to thenaturally occurring ketoreductase of L. kefir represented by SEQ IDNO:2. These differences occur at residue positions that can affectenzyme activity, stereoselectivity, thermostability, solvent stability,polypeptide expression, co-factor affinity, or various combinationsthereof. In particular, the engineered polypeptides can have one or moreresidue difference as compared to SEQ ID NO:2 at the following residuepositions: X17, X25, X29, X40, X43, X64, X71, X76, X80, X87, X94, X95,X96, X131, X144, X145, X147, X150, X152, X153, X157, X173, X190, X194,X195, X196, X199, X200, X226, X233, and X249. Guidance on amino acidresidues that can be present at these positions as well as combinationsof residue differences useful for generating enzymes with improvedproperties are described in detail in the descriptions herein.

In some embodiments, the engineered ketoreductase polypeptides capableof converting compound (2c) or a structural analog thereof to compound(1c) or corresponding structural analog in enantiomeric excess,comprises an amino acid sequence that has at least 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequenceidentity to a reference polypeptide selected from SEQ ID NO:6, 8, 10,12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38.

In some embodiments, the non-naturally occurring ketoreductasepolypeptide for use in the processes disclosed herein and capable ofconverting compound (2c) or structural analog thereof to compound (1c)or corresponding structural analog in enantiomeric excess with activitythat is equal to or with at least 2-fold, at least 10-fold, at least15-fold, at least 20-fold, at least 25-fold, at least 30-fold, or atleast 35-fold or more activity of the polypeptide of SEQ ID NO:4comprises an amino acid sequence that has at least 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identityto a reference amino acid sequence selected from any one of SEQ ID NO:4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, or 38,with the proviso that the amino acid sequence comprises any one of theset of residue differences as compared to SEQ ID NO: 2 contained in anyone of the polypeptide sequences of SEQ ID NO:4 to SEQ ID NO:38 listedin Table 3. In some embodiments, in addition to the set of amino acidresidue differences of any one of the non-naturally occurringpolypeptides of SEQ ID NO: 4 to SEQ ID NO: 38, the sequence of thenon-naturally occurring polypeptide can further comprise 1-2, 1-3, 1-4,1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20,1-22, 1-24, 1-26, 1-30, 1-35, 1-40 residue differences at other aminoacid residue positions as compared to the SEQ ID NO: 2. In someembodiments, the residue differences can comprise conservativesubstitutions and non-conservative substitutions as compared to SEQ IDNO: 2.

In some embodiments, the ketoreductase capable of converting compound(2c) or structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess and having the specifiedsequence identity to any of the reference polypeptides described herein,has an amino acid sequence that comprises at least the followingfeatures: X80 is T; X96 is V or R; X145 is L; X153 is T; X190 is P; X196is L or M; and X226 is V.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at residue positions X80, X96, X145, X153, X190,X196, and X226, further comprises one or more of the following features:X71 is P or G; X87 is L; and X131 is C.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at residue positions X80, X96, X145, X153, X190,X196, and X226, and X71, X87, and X131 above can further comprise one ormore of the following features: X17 is H or M; X29 is T; X40 is R; X43is R or V; X64 is V; X94 is G; X95 is Y or M; X147 is Q or M; X152 is Lor A; X173 is L; X199 is M; and X200 is P.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at the residue positions indicated above can furthercomprise one or more of the following features: X25 is T; X76 is A; X144is V; X150 is L; X157 is C or S;

X194 is R; X233 is G; and X249 is W or F.

In some embodiments, the ketoreductase capable of converting compound(2c) or structural analog to compound (1c) or corresponding structuralanalog in enantiomeric excess and having the specified sequence identityto any of the reference polypeptides, has an amino acid sequence thatcomprises at least the following features: X64 is V; X71 is P; X80 is T;X87 is L; X94 is A or G; X96 is V; X145 is L; X147 is Q or M; X153 is T;X173 is L; X190 is P; X196 is M; X199 is M; and X226 is V.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at residue positions X64, X71, X80, X87, X94, X96,X145, X147, X153, X173, X190, X196, X199 and X226, further comprises oneor more of the following features: X17 is M or H; X29 is T; X40 is R;X43 is R or V; X95 is M or Y; X131 is C; X152 is L or A; and X200 is P.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at the residue positions indicated above can furthercomprise one or more of the following features: X25 is T; X76 is A; X144is V; X150 is L; X157 is C or S; X194 is R; X233 is G; and X249 is W orF.

In some embodiments, the ketoreductase capable of converting compound(2c) or structural analog to compound (1c) or corresponding structuralanalog in enantiomeric excess and having the specified sequence identityto any of the reference polypeptides, has an amino acid sequence thatcomprises at least the following features: X17 is H or M; X25 is T; X29is T; X40 is R; X43 is R or V; X64 is V; X71 is G or P; X80 is T; X87 isL; X94 is G; X95 is Y or M; X96 is R or V; X131 is C; X145 is L; X147 isQ or M; X152 is A or L; X153 is T; X157 is S or C; X173 is L; X190 is P;X196 is M or L; X199 is M; X200 is P; and X226 is V.

In some embodiments, the ketoreductase with the preceding specifiedfeatures can further comprise one or more of the following features: X76is A; X144 is V; X150 is L; X194 is R; X233 is G; and X249 is W or F.

In some embodiments, the non-naturally occurring ketoreductasepolypeptides capable of converting compound (2c) or structural analogthereof to compound (1c) or corresponding structural analog, comprisesan amino acid sequence selected from SEQ ID NO: 6, 8, 10, 12, 14, 16,18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38.

In another aspect, an engineered ketoreductase polypeptide comprises anamino acid sequence that has at least 80%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity tothe reference polypeptide of SEQ ID NO:2 and comprises at least one ormore residue differences as compared to SEQ ID NO:2 at residue positionsX71, X87 and X131, wherein the polypeptide has ketoreductase activity.

In another aspect, the present disclosure provides polynucleotidesencoding the ketoreductase polypeptide capable of converting compound(2c) to compound (1c) in enantiomeric excess, expression vectorscomprising the polynucleotides, and host cells capable of expressing thepolynucleotides encoding the engineered polypeptides.

In a further aspect, the present disclosure also provides method ofmanufacturing the engineered ketoreductase polypeptides, where themethod comprises culturing a host cell capable of expressing theengineered ketoreductase polypeptide under culture conditions suitablefor expression of the polypeptide. The method can further compriseisolating the expressed polypeptide.

5. DETAILED DESCRIPTION

The synthesis of eslicarbazepine, also known S-licarbazepine and havingthe chemical name(S)-10-hydroxy-10,11-dihydro-5h-dibenzo[b,f]azepine-5-carboxamide, hasbeen carried out using chemical procedures, such as by chiral separationof S-licarbazepine from R-licarbazepine or by chiral synthesis ofS-licarbazepine. See, e.g., US2007119197, WO02092572, WO2007117166,WO2007012793, and WO2010113179. As noted above, chemical synthesis canbe circumvented by employing carbonyl reductases (e.g., ketoreductases)to enzymatically reduce oxcarbazepine to the corresponding chiralalcohol. However, some ketoreductases produce R-licarbazepine inenantiomeric excess while other ketoreductases produce S-licarbazepinein enantiomeric excess (see Publication IPCOM000193904D). The referenceIPCOM000193904D did not describe the features that distinguish aketoreductase with stereoselectivity for S-licarbazepine fromketoreductases with stereoselectivity for R-licarbazepine. It is nowshown herein that ketoreductases derived from a ketoreductase ofLactobacillus are capable of converting oxcarbazepine to eslicarbazepinein enantiomeric excess. Based on this finding, other engineeredketoreductases have been developed that are capable of efficientlyconverting oxcarbazepine to eslicarbazepine in ≧90% enantiomeric excess,including engineered ketoreductases capable of >90% conversion ofoxcarbazepine at a substrate loading of about 50 to about 100 g/L toeslicarbazepine in ≧99% enantiomeric excess within 24 h.

For the descriptions herein and the appended claims, the singular forms“a”, “an” and “the” include plural referents unless the context clearlyindicates otherwise. Thus, for example, reference to “a polypeptide”includes more than one polypeptide, and reference to “a compound” refersto more than one compound.

It is to be further understood that where descriptions of variousembodiments use the term “comprising,” those skilled in the art wouldunderstand that in some specific instances, an embodiment can bealternatively described using language “consisting essentially of” or“consisting of.”

Also, the use of “or” means “and/or” unless stated otherwise. Similarly,“comprise,” “comprises,” “comprising” “include,” “includes,”“including,” “has,” “have,” and “having” are interchangeable and notintended to be limiting.

The foregoing general description and the detailed description areexemplary and explanatory only and are not restrictive of thisdisclosure.

5.1 DEFINITIONS

In reference to the present disclosure, the technical and scientificterms used in the descriptions herein will have the meanings commonlyunderstood by one of ordinary skill in the art, unless specificallydefined otherwise. Accordingly, the following terms are intended to havethe following meanings:

“Protein,” “polypeptide,” and “peptide” are used interchangeably hereinto denote a polymer of at least two amino acids covalently linked by anamide bond, regardless of length or post-translational modification(e.g., glycosylation, phosphorylation, lipidation, myristilation,ubiquitination, etc.). Included within this definition are D- andL-amino acids, and mixtures of D- and L-amino acids.

“Coding sequence” refers to that portion of a nucleic acid (e.g., agene) that encodes an amino acid sequence of a protein.

“Naturally occurring” or “wild-type” refers to the form found in nature.For example, a naturally occurring or wild-type polypeptide orpolynucleotide sequence is a sequence present in an organism that can beisolated from a source in nature and which has not been intentionallymodified by human manipulation.

“Non-naturally occurring” or “engineered” or “recombinant” when used inthe present disclosure with reference to, e.g., a cell, nucleic acid, orpolypeptide, refers to a material, or a material corresponding to thenatural or native form of the material, that has been modified in amanner that would not otherwise exist in nature, or is identical theretobut produced or derived from synthetic materials and/or by manipulationusing recombinant techniques. Non-limiting examples include, amongothers, recombinant cells expressing genes that are not found within thenative (non-recombinant) form of the cell or express native genes thatare otherwise expressed at a different level.

“Percentage of sequence identity,” “percent identity,” and “percentidentical” are used herein to refer to comparisons betweenpolynucleotide sequences or polypeptide sequences, and are determined bycomparing two optimally aligned sequences over a comparison window,wherein the portion of the polynucleotide or polypeptide sequence in thecomparison window may comprise additions or deletions (i.e., gaps) ascompared to the reference sequence for optimal alignment of the twosequences. The percentage is calculated by determining the number ofpositions at which either the identical nucleic acid base or amino acidresidue occurs in both sequences or a nucleic acid base or amino acidresidue is aligned with a gap to yield the number of matched positions,dividing the number of matched positions by the total number ofpositions in the window of comparison and multiplying the result by 100to yield the percentage of sequence identity. Determination of optimalalignment and percent sequence identity is performed using the BLAST andBLAST 2.0 algorithms (see e.g., Altschul et al., 1990, J. Mol. Biol.215: 403-410 and Altschul et al., 1977, Nucleic Acids Res. 3389-3402).Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information website.

Briefly, the BLAST analyses involve first identifying high scoringsequence pairs (HSPs) by identifying short words of length W in thequery sequence, which either match or satisfy some positive-valuedthreshold score T when aligned with a word of the same length in adatabase sequence. T is referred to as, the neighborhood word scorethreshold (Altschul et al, supra). These initial neighborhood word hitsact as seeds for initiating searches to find longer HSPs containingthem. The word hits are then extended in both directions along eachsequence for as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always >0)and N (penalty score for mismatching residues; always <0). For aminoacid sequences, a scoring matrix is used to calculate the cumulativescore. Extension of the word hits in each direction are halted when: thecumulative alignment score falls off by the quantity X from its maximumachieved value; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) of 10, M=5, N=−4, and a comparison of bothstrands. For amino acid sequences, the BLASTP program uses as defaults awordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoringmatrix (see Henikoff and Henikoff, 1989, Proc Natl Acad Sci USA89:10915).

Numerous other algorithms are available that function similarly to BLASTin providing percent identity for two sequences. Optimal alignment ofsequences for comparison can be conducted, e.g., by the local homologyalgorithm of Smith and Waterman, 1981, Adv. Appl. Math. 2:482, by thehomology alignment algorithm of Needleman and Wunsch, 1970, J. Mol.Biol. 48:443, by the search for similarity method of Pearson and Lipman,1988, Proc. Natl. Acad. Sci. USA 85:2444, by computerizedimplementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA inthe GCG Wisconsin Software Package), or by visual inspection (seegenerally, Current Protocols in Molecular Biology, F. M. Ausubel et al.,eds., Current Protocols, a joint venture between Greene PublishingAssociates, Inc. and John Wiley & Sons, Inc., (1995 Supplement)(Ausubel)). Additionally, determination of sequence alignment andpercent sequence identity can employ the BESTFIT or GAP programs in theGCG Wisconsin Software package (Accelrys, Madison Wis.), using defaultparameters provided.

“Reference sequence” refers to a defined sequence to which anothersequence is compared. A reference sequence may be a subset of a largersequence, for example, a segment of a full-length gene or polypeptidesequence. Generally, a reference sequence is at least 20 nucleotide oramino acid residues in length, at least 25 residues in length, at least50 residues in length, or the full length of the nucleic acid orpolypeptide. Since two polynucleotides or polypeptides may each (1)comprise a sequence (i.e., a portion of the complete sequence) that issimilar between the two sequences, and (2) may further comprise asequence that is divergent between the two sequences, sequencecomparisons between two (or more) polynucleotides or polypeptide aretypically performed by comparing sequences of the two polynucleotidesover a comparison window to identify and compare local regions ofsequence similarity. The term “reference sequence” is not intended to belimited to wild-type sequences, and can include engineered or alteredsequences. For example, in some embodiments, a “reference sequence” canbe a previously engineered or altered amino acid sequence.

“Comparison window” refers to a conceptual segment of at least about 20contiguous nucleotide positions or amino acids residues wherein asequence may be compared to a reference sequence of at least 20contiguous nucleotides or amino acids and wherein the portion of thesequence in the comparison window may comprise additions or deletions(i.e., gaps) of 20 percent or less as compared to the reference sequence(which does not comprise additions or deletions) for optimal alignmentof the two sequences. The comparison window can be longer than 20contiguous residues, and includes, optionally 30, 40, 50, 100, or longerwindows.

“Corresponding to”, “reference to” or “relative to” when used in thecontext of the numbering of a given amino acid or polynucleotidesequence refers to the numbering of the residues of a specifiedreference sequence when the given amino acid or polynucleotide sequenceis compared to the reference sequence. In other words, the residuenumber or residue position of a given polymer is designated with respectto the reference sequence rather than by the actual numerical positionof the residue within the given amino acid or polynucleotide sequence.For example, a given amino acid sequence, such as that of an engineeredketoreductase, can be aligned to a reference sequence by introducinggaps to optimize residue matches between the two sequences. In thesecases, although the gaps are present, the numbering of the residue inthe given amino acid or polynucleotide sequence is made with respect tothe reference sequence to which it has been aligned. As used herein, areference to a residue position, such as “Xn’ as further describedbelow, is to be construed as referring to “a residue corresponding to”,unless specifically denoted otherwise.

“Stereoselectivity” refers to the preferential formation in a chemicalor enzymatic reaction of one stereoisomer over another.Stereoselectivity can be partial, where the formation of onestereoisomer is favored over the other, or it may be complete where onlyone stereoisomer is formed. When the stereoisomers are enantiomers, thestereoselectivity is referred to as enantioselectivity, the fraction(typically reported as a percentage) of one enantiomer in the sum ofboth. It is commonly alternatively reported in the art (typically as apercentage) as the enantiomeric excess (e.e.) calculated therefromaccording to the formula [major enantiomer−minor enantiomer]/[majorenantiomer+minor enantiomer]. Where the stereoisomers arediastereoisomers, the stereoselectivity is referred to asdiastereoselectivity, the fraction (typically reported as a percentage)of one diastereomer in a mixture of two diastereomers, commonlyalternatively reported as the diastereomeric excess (d.e.). Enantiomericexcess and diastereomeric excess are types of stereomeric excess.

“Highly stereoselective” refers to a chemical or enzymatic reaction thatis capable of converting a substrate, e.g., compound (2c), to itscorresponding chiral alcohol product, e.g., compound (1c), with at leastabout 85% stereomeric excess.

“Increased enzymatic activity” or “increased activity” refers to animproved property of an engineered enzyme, which can be represented byan increase in specific activity (e.g., product produced/time/weightprotein) or an increase in percent conversion of the substrate to theproduct (e.g., percent conversion of starting amount of substrate toproduct in a specified time period using a specified amount ofketoreductase) as compared to a reference enzyme. Exemplary methods todetermine enzyme activity are provided in the Examples. Any propertyrelating to enzyme activity may be affected, including the classicalenzyme properties of K_(m), V_(max) or k_(cat), changes of which canlead to increased enzymatic activity. The ketoreductase activity can bemeasured by any one of standard assays used for measuringketoreductases, such as change in substrate or product concentration, orchange in concentration of the cofactor (in absence of a cofactorregenerating system). Comparisons of enzyme activities are made using adefined preparation of enzyme, a defined assay under a set condition,and one or more defined substrates, as further described in detailherein. Generally, when enzymes in cell lysates are compared, thenumbers of cells and the amount of protein assayed are determined aswell as use of identical expression systems and identical host cells tominimize variations in amount of enzyme produced by the host cells andpresent in the lysates.

“Conversion” refers to the enzymatic transformation of a substrate tothe corresponding product. “Percent conversion” refers to the percent ofthe substrate that is converted to the product within a period of timeunder specified conditions. Thus, for example, the “enzymatic activity”or “activity” of a ketoreductase polypeptide can be expressed as“percent conversion” of the substrate to the product.

“Thermostable” or “thermal stable” are used interchangeably to refer toa polypeptide that is resistant to inactivation when exposed to a set oftemperature conditions (e.g., 40-80° C.) for a period of time (e.g.,0.5-24 hrs) compared to the untreated enzyme, thus retaining a certainlevel of residual activity (e.g., more than 60% to 80% for example)after exposure to elevated temperatures.

“Solvent stable” refers to the ability of a polypeptide to maintainsimilar activity (e.g., more than e.g., 60% to 80%) after exposure tovarying concentrations (e.g. 5-99%) of solvent (e.g., isopropylalcohol,tetrahydrofuran, 2-methyltetrahydrofuran, acetone, toluene,butylacetate, methyl tert-butylether, etc.) for a period of time (e.g.,0.5-24 hrs) compared to the untreated enzyme.

“Acidic Amino Acid or Residue” refers to a hydrophilic amino acid orresidue having a side chain exhibiting a pK value of less than about 6when the amino acid is included in a peptide or polypeptide. Acidicamino acids typically have negatively charged side chains atphysiological pH due to loss of a hydrogen ion. Genetically encodedacidic amino acids include Glu (E) and Asp (D).

“Basic Amino Acid or Residue” refers to a hydrophilic amino acid orresidue having a side chain exhibiting a pK value of greater than about6 when the amino acid is included in a peptide or polypeptide. Basicamino acids typically have positively charged side chains atphysiological pH due to association with hydronium ion. Geneticallyencoded basic amino acids include Arg (R) and Lys (K).

“Polar Amino Acid or Residue” refers to a hydrophilic amino acid orresidue having a side chain that is uncharged at physiological pH, butwhich has at least one bond in which the pair of electrons shared incommon by two atoms is held more closely by one of the atoms.Genetically encoded polar amino acids include Asn (N), Gln (Q), Ser (S)and Thr (T).

“Hydrophobic Amino Acid or Residue” refers to an amino acid or residuehaving a side chain exhibiting a hydrophobicity of greater than zeroaccording to the normalized consensus hydrophobicity scale of Eisenberget al., 1984, J. Mol. Biol. 179:125-142. Genetically encoded hydrophobicamino acids include Pro (P), Ile (I), Phe (F), Val (V), Leu (L), Trp(W), Met (M), Ala (A) and Tyr (Y).

“Aromatic Amino Acid or Residue” refers to a hydrophilic or hydrophobicamino acid or residue having a side chain that includes at least onearomatic or heteroaromatic ring. Genetically encoded aromatic aminoacids include Phe (F), Tyr (Y) and Trp (W). Although owing to the itsheteroaromatic ring side chain His (H) is classified as an aromaticresidue, it may also be classified as a basic residue owing to pKa ofits heteroaromatic nitrogen atom.

“Non-polar Amino Acid or Residue” refers to a hydrophobic amino acid orresidue having a side chain that is uncharged at physiological pH andwhich has bonds in which the pair of electrons shared in common by twoatoms is generally held equally by each of the two atoms (i.e., the sidechain is not polar). Genetically encoded non-polar amino acids includeGly (G), Leu (L), Val (V), Ile (I), Met (M) and Ala (A).

“Aliphatic Amino Acid or Residue” refers to a hydrophobic amino acid orresidue having an aliphatic hydrocarbon side chain. Genetically encodedaliphatic amino acids include Ala (A), Val (V), Leu (L) and Ile (I).

The amino acid Cys (C) is unique in that it can form disulfide bridgeswith other Cys (C) amino acids or other sulfanyl- orsulfhydryl-containing amino acids. The ability of Cys (and other aminoacids with —SH containing side chains) to exist in a polypeptide ineither the reduced free —SH or oxidized disulfide-bridged form affectswhether it contributes net hydrophobic or hydrophilic character to thepolypeptide. While Cys exhibits a hydrophobicity of 0.29 according tothe normalized consensus scale of Eisenberg (Eisenberg et al., 1984,supra), it is to be understood that for purposes of the presentdisclosure, Cys is classified into its own unique group.

The amino acid Pro (P) has a conformationally constrained nature.Although it has hydrophobic properties, as used herein, Pro (P) or othersimilar residues is classified as a “conformationally constrained.”

“Hydroxyl-containing Amino Acid or Residue” refers to an amino acid orresidue containing a hydroxyl (—OH) moiety. Genetically-encodedhydroxyl-containing amino acids include Ser (S) and Thr (T). While L-Tyr(Y) contains a hydroxyl moiety, it is classified herein as an aromaticamino acid or residue.

“Amino acid difference” or “residue difference” refers to a change inthe residue at a specified position of a polypeptide sequence whencompared to a reference sequence. For example, a residue difference atposition X80, where the reference sequence has an alanine, refers to achange of the residue at position X80 to any residue other than alanine.As disclosed herein, an enzyme can include one or more residuedifferences relative to a reference sequence, where multiple residuedifferences typically are indicated by a list of the specified positionswhere changes are made relative to the reference sequence. The residuedifferences can be non-conservative changes or conservative changes. Insome embodiments, the residue differences can be conservativesubstitutions, non-conservative substitutions, or a combination ofnon-conservative and conservative substitutions. For the descriptions ofthe non-naturally occurring polypeptides herein, the amino acid residueposition in the reference sequence is determined in the ketoreductasepolypeptide beginning from the initiating methionine (M) residue (i.e.,M represents residue position 1), although it will be understood by theskilled artisan that this initiating methionine residue may be removedby biological processing machinery, such as in a host cell or in vitrotranslation system, to generate a mature protein lacking the initiatingmethionine residue. The polypeptide sequence position at which aparticular amino acid or amino acid change (“residue difference”) ispresent is sometimes described herein as “Xn”, or “position n”, where nrefers to the residue position with respect to the reference sequence.Where applicable, a specific substitution mutation, which is areplacement of the specific residue in a reference sequence with adifferent specified residue may be denoted by the conventional notation“X(number)Y”, where X is the single letter identifier of the residue inthe reference sequence, “number” is the residue position in thereference sequence, and Y is the single letter identifier of the residuesubstitution in the engineered sequence.

“Conservative amino acid substitutions” refer to the interchangeabilityof residues having similar side chains, and thus typically involvessubstitution of the amino acid in the polypeptide with amino acidswithin the same or similar defined class of amino acids. By way ofexample and not limitation, an amino acid with an aliphatic side chainmay be substituted with another aliphatic amino acid, e.g., alanine,valine, leucine, and isoleucine; an amino acid with hydroxyl side chainis substituted with another amino acid with a hydroxyl side chain, e.g.,serine and threonine; an amino acids having aromatic side chains issubstituted with another amino acid having an aromatic side chain, e.g.,phenylalanine, tyrosine, tryptophan, and histidine; an amino acid with abasic side chain is substituted with another amino acid with a basisside chain, e.g., lysine and arginine; an amino acid with an acidic sidechain is substituted with another amino acid with an acidic side chain,e.g., aspartic acid or glutamic acid; and a hydrophobic or hydrophilicamino acid is replaced with another hydrophobic or hydrophilic aminoacid, respectively. Exemplary conservative substitutions are provided inTable 1.

TABLE 1 Residue Possible Conservative Substitutions A, L, V, I Otheraliphatic (A, L, V, I) Other non-polar (A, L, V, I, G, M) G, M Othernon-polar (A, L, V, I, G, M) D, E Other acidic (D, E) K, R Other basic(K, R) N, Q, S, T Other polar H, Y, W, F Other aromatic (H, Y, W, F) C,P None

“Non-conservative substitution” refers to substitution of an amino acidin the polypeptide with an amino acid with significantly differing sidechain properties. Non-conservative substitutions may use amino acidsbetween, rather than within, the defined groups and affects (a) thestructure of the peptide backbone in the area of the substitution (e.g.,proline for glycine) (b) the charge or hydrophobicity, or (c) the bulkof the side chain. By way of example and not limitation, an exemplarynon-conservative substitution can be an acidic amino acid substitutedwith a basic or aliphatic amino acid; an aromatic amino acid substitutedwith a small amino acid; and a hydrophilic amino acid substituted with ahydrophobic amino acid.

“Deletion” refers to modification of the polypeptide by removal of oneor more amino acids from the reference polypeptide. Deletions cancomprise removal of 1 or more amino acids, 2 or more amino acids, 5 ormore amino acids, 10 or more amino acids, 15 or more amino acids, or 20or more amino acids, up to 10% of the total number of amino acids, or upto 20% of the total number of amino acids making up the polypeptidewhile retaining enzymatic activity and/or retaining the improvedproperties of an engineered enzyme. Deletions can be directed to theinternal portions and/or terminal portions of the polypeptide. Invarious embodiments, the deletion can comprise a continuous segment orcan be discontinuous.

“Insertion” refers to modification of the polypeptide by addition of oneor more amino acids to the reference polypeptide. In some embodiments,the improved engineered ketoreductase enzymes comprise insertions of oneor more amino acids to the naturally occurring ketoreductase polypeptideas well as insertions of one or more amino acids to other improvedketoreductase polypeptides. Insertions can be in the internal portionsof the polypeptide, or to the carboxy or amino terminus. Insertions asused herein include fusion proteins as is known in the art. Theinsertion can be a contiguous segment of amino acids or separated by oneor more of the amino acids in the naturally occurring polypeptide.

“Fragment” as used herein refers to a polypeptide that has anamino-terminal and/or carboxy-terminal deletion, but where the remainingamino acid sequence is identical to the corresponding positions in thesequence. Fragments can typically have about 80%, 90%, 95%, 98%, and 99%of the full-length ketoreductase polypeptide, for example thepolypeptide of SEQ ID NO:4.

“Isolated polypeptide” refers to a polypeptide which is substantiallyseparated from other contaminants that naturally accompany it, e.g.,protein, lipids, and polynucleotides. The term embraces polypeptideswhich have been removed or purified from their naturally-occurringenvironment or expression system (e.g., host cell or in vitrosynthesis). The improved ketoreductase enzymes may be present within acell, present in the cellular medium, or prepared in various forms, suchas lysates or isolated preparations. As such, in some embodiments, theengineered ketoreductase polypeptides of the present disclosure can bean isolated polypeptide.

“Substantially pure polypeptide” refers to a composition in which thepolypeptide species is the predominant species present (i.e., on a molaror weight basis it is more abundant than any other individualmacromolecular species in the composition), and is generally asubstantially purified composition when the object species comprises atleast about 50 percent of the macromolecular species present by mole or% weight. Generally, a substantially pure engineered ketoreductasepolypeptide composition will comprise about 60% or more, about 70% ormore, about 80% or more, about 90% or more, about 95% or more, and about98% or more of all macromolecular species by mole or % weight present inthe composition. Solvent species, small molecules (<500 Daltons), andelemental ion species are not considered macromolecular species. In someembodiments, the isolated improved ketoreductase polypeptide is asubstantially pure polypeptide composition.

“Heterologous” polynucleotide refers to any polynucleotide that isintroduced into a host cell by laboratory techniques, and includespolynucleotides that are removed from a host cell, subjected tolaboratory manipulation, and then reintroduced into a host cell.

“Codon optimized” refers to changes in the codons of the polynucleotideencoding a protein to those preferentially used in a particular organismsuch that the encoded protein is efficiently expressed in the organismof interest. In some embodiments, the polynucleotides encoding theketoreductase enzymes may be codon optimized for optimal production fromthe host organism selected for expression.

“Control sequence” is defined herein to include all components, whichare necessary or advantageous for the expression of a polynucleotideand/or polypeptide of the present disclosure. Each control sequence maybe native or foreign to the polynucleotide of interest. Such controlsequences include, but are not limited to, a leader, polyadenylationsequence, propeptide sequence, promoter, signal peptide sequence, andtranscription terminator.

“Operably linked” is defined herein as a configuration in which acontrol sequence is appropriately placed (i.e., in a functionalrelationship) at a position relative to a polynucleotide of interestsuch that the control sequence directs or regulates the expression ofthe polynucleotide and/or polypeptide of interest.

“Cofactor regeneration system” or “cofactor recycling system” refers toa set of reactants that participate in a reaction that reduces theoxidized form of the cofactor (e.g., NADP+ to NADPH). Cofactors oxidizedby the ketoreductase-catalyzed reduction of the keto substrate areregenerated in reduced form by the cofactor regeneration system.Cofactor regeneration systems comprise a stoichiometric reductant thatis a source of reducing hydrogen equivalents and is capable of reducingthe oxidized form of the cofactor. The cofactor regeneration system mayfurther comprise a catalyst, for example an enzyme catalyst thatcatalyzes the reduction of the oxidized form of the cofactor by thereductant. Cofactor regeneration systems to regenerate NADH or NADPHfrom NAD+ or NADP+, respectively, are known in the art and may be usedin the methods described herein.

“Glucose dehydrogenase” and “GDH” are used interchangeably herein torefer to an NAD+ or NADP+-dependent enzyme that catalyzes the conversionof D-glucose and NAD+ or NADP+ to gluconic acid and NADH or NADPH,respectively.

“Secondary alcohol dehydrogenase” is used herein to refer to an NAD+ orNADP+-dependent enzyme that catalyzes the conversion of a secondaryalcohol (e.g., isopropanol) and NAD+ or NADP+ to a ketone and NADH orNADPH, respectively.

“Suitable reaction conditions” refers to those conditions in thebiocatalytic reaction solution (e.g., ranges of enzyme loading,substrate loading, cofactor loading, temperature, pH, buffers,co-solvents, etc.) under which a ketoreductase polypeptide of thepresent disclosure is capable of converting compound (2c) to compound(1c). Exemplary “suitable reaction conditions” are provided in thepresent disclosure and illustrated by the Examples.

“Loading”, such as in “compound loading” or “enzyme loading” refers tothe concentration or amount of a component in a reaction mixture at thestart of the reaction.

“Structural analog” refers to a chemical compound having a structuresimilar to that of a reference compound but differing in one or moreatoms, functional groups or substructures.

“Substrate” in the context of a biocatalyst mediated process refers tothe compound or molecule acted on by the biocatalyst. For example, anexemplary substrate for the ketoreductase biocatalyst in the processdisclosed herein is compound (2c).

“Product” in the context of a biocatalyst mediated process refers to thecompound or molecule resulting from the action of the biocatalyst. Forexample, an exemplary product for the ketoreductase biocatalyst in theprocess disclosed herein is compound (1c).

“Alkyl” refers to groups of from 1 to 18 carbon atoms inclusively,either straight chained or branched, more preferably from 1 to 8 carbonatoms inclusively, and most preferably 1 to 6 carbon atoms inclusively.An alkyl with a specified number of carbon atoms is denoted inparenthesis, e.g., (C1-C4)alkyl refers to an alkyl of 1 to 4 carbonatoms.

“Alkenyl” refers to groups of from 2 to 12 carbon atoms inclusively,either straight or branched containing at least one double bond butoptionally containing more than one double bond.

“Alkynyl” refers to groups of from 2 to 12 carbon atoms inclusively,either straight or branched containing at least one triple bond butoptionally containing more than one triple bond, and additionallyoptionally containing one or more double bonded moieties.

“Alkoxy” refers to the group alkyl-O— wherein the alkyl group is asdefined above including optionally substituted alkyl groups as alsodefined above.

“Aryl” refers to an unsaturated aromatic carbocyclic group of from 6 to14 carbon atoms inclusively having a single ring (e.g., phenyl) ormultiple condensed rings (e.g., naphthyl or anthryl). Exemplary arylsinclude phenyl, pyridyl, naphthyl and the like.

“Arylalkyl” refers to aryl-alkyl-groups preferably having from 1 to 6carbon atoms inclusively in the alkyl moiety and from 6 to 14 carbonatoms inclusively in the aryl moiety. Such arylalkyl groups areexemplified by benzyl, phenethyl and the like.

“Cycloalkyl” refers to cyclic alkyl groups of from 3 to 12 carbon atomsinclusively having a single cyclic ring or multiple condensed ringswhich can be optionally substituted with from 1 to 3 alkyl groups. suchcycloalkyl groups include, by way of example, single ring structuressuch as cyclopropyl, cyclobutyl, cyclopentyl, cyclooctyl,1-methylcyclopropyl, 2-methylcyclopentyl, 2-methylcyclooctyl, and thelike, or multiple ring structures, including bridged ring systems, suchas adamantyl, and the like.

“Cycloalkylalkyl” refers to cycloalkyl-alkyl-groups preferably havingfrom 1 to 6 carbon atoms inclusively in the alkyl moiety and from 6 to10 carbon atoms inclusively in the cycloalkyl moiety. Suchcycloalkylalkyl groups are exemplified by cyclopropylmethyl,cyclohexylethyl and the like.

“Bridged ring system” refers to a bicyclic or polycyclic ring system inwhich at least two rings have more than two common atoms. Such a systemmay contain isolated or conjugated unsaturation.

“Amino” refers to the group —NH₂. Substituted amino refers to the group—NHR′, NR′R′, and NR′R′R′, where each R′ is independently selected fromsubstituted or unsubstituted alkyl, cycloalkyl, cycloheteroalkyl,alkoxy, aryl, heteroaryl, heteroarylalkyl, acyl, alkoxycarbonyl,sulfanyl, sulfinyl, sulfonyl, and the like. Typical amino groupsinclude, but are limited to, dimethylamino, diethylamino,trimethylammonium, triethylammonium, methylysulfonylamino,furanyl-oxy-sulfamino, and the like.

“Alkylamino” refers to a —NHR′ group, where R is an alkyl, an N-oxidederivative, or a protected derivative thereof, e.g., methylamino,ethylamino, n-propylamino, iso-propylamino, n-butylamino,iso-butylamino, tert-butylamino, or methylamino-N-oxide, and the like.

“Aminoalkyl” refers to an alkyl group in which one or more of thehydrogen atoms is replaced with an amino group as defined herein,including a substituted amino group.

“Carboxy” refers to —COOH.

“Carbonyl” refers to —C(O)—, which may have a variety of substituents toform different carbonyl groups including acids, acid halides, aldehydes,amides, esters, and ketones.

“Alkyloxycarbonyl” refers to —C(O)OR′, where R′ is an alkyl, which canbe optionally substituted.

“Aminocarbonyl” refers to —C(O)NH₂. Substituted aminocarbonyl refers to—C(O)NR′R′, where the amino group NR′R′ is as defined herein.

“Thiocarbonyl” refers to —C(S)—. Substituted thiocarbonyl refers to—C(S)R′, where R′ is a suitable substituent as described below.

“Aminothiocarbonyl” refers to a —C(S)NR′R′, where the amino group —NR′R′is as defined herein.

“Halogen” or “halo” refers to fluoro, chloro, bromo and iodo.

“Hydroxy” refers to —OH.

“Cyano” refers to —CN.

“Sulfonyl” refers to —SO₂—. Substituted sulfonyl refers to —SO₂R′, whereR′ is a suitable substituent as described below.

“Aminosulfonyl” refers to —SO₂NH₂. Substituted aminosulfonyl refers to—SO₂NR′R′, where the amino group —NR′R′ is as defined herein.

“Haloalkyl” refers to an alkyl group in which one or more of thehydrogen atoms is replaced with a halogen. Thus, the term “haloalkyl” ismeant to include monohaloalkyls, dihaloalkyls, trihaloalkyls, etc. up toperhaloalkyls. For example, the expression “(C1C2) haloalkyl” includes1-fluoromethyl, difluoromethyl, trifluoromethyl, 1-fluoroethyl,1,1-difluoroethyl, 1,2-difluoroethyl, 1,1,1 trifluoroethyl,perfluoroethyl, etc.

“Heteroaryl” refers to a monovalent aromatic heterocyclic group of from1 to 10 carbon atoms inclusively and 1 to 4 heteroatoms inclusivelyselected from oxygen, nitrogen and sulfur within the ring. Suchheteroaryl groups can have a single ring (e.g., pyridyl or furyl) ormultiple condensed rings (e.g., indolizinyl or benzothienyl).

“Heteroarylalkyl” refers to heteroaryl-alkyl-groups preferably havingfrom 1 to 6 carbon atoms inclusively in the alkyl moiety and from 6 to10 atoms inclusively in the heteroaryl moiety. Such heteroarylalkylgroups are exemplified by pyridylmethyl and the like.

“Heteroarylalkenyl” refers to heteroaryl-alkenyl-groups preferablyhaving from 2 to 6 carbon atoms inclusively in the alkenyl moiety andfrom 6 to 10 atoms inclusively in the heteroaryl moiety.

“Heteroarylalkynyl” refers to heteroaryl-alkynyl-groups preferablyhaving from 2 to 6 carbon atoms inclusively in the alkynyl moiety andfrom 6 to 10 atoms inclusively in the heteroaryl moiety.

“Heterocycle” and interchangeably “heterocycloalkyl” refer to asaturated or unsaturated group having a single ring or multiplecondensed rings, from 1 to 8 carbon atoms inclusively and from 1 to 4hetero atoms inclusively selected from nitrogen, sulfur or oxygen withinthe ring. Such heterocyclic groups can have a single ring (e.g.,piperidinyl or tetrahydrofuryl) or multiple condensed rings (e.g.,indolinyl, dihydrobenzofuran or quinuclidinyl). Examples of heterocyclesand heteroaryls include, but are not limited to, furan, thiophene,thiazole, oxazole, pyrrole, imidazole, pyrazole, pyridine, pyrazine,pyrimidine, pyridazine, indolizine, isoindole, indole, indazole, purine,quinolizine, isoquinoline, quinoline, phthalazine, naphthylpyridine,quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline,phenanthridine, acridine, phenanthroline, isothiazole, phenazine,isoxazole, phenoxazine, phenothiazine, imidazolidine, imidazoline,piperidine, piperazine, pyrrolidine, indoline and the like.

Bicycloalkyl” refers to two saturated or partially unsaturated fused orbridged polycyclic ring system with two or more common atoms. A “bridgedbicycloalkyl ring system” refers to two saturated or partiallyunsaturated rings with more than two common atoms.

“Heterobicycloalkyl” refers to a bicycloalkyl in which 1 to 4 atomswithin the ring is a heteroatom, inclusively selected from nitrogen,sulfur or oxygen. A “bridged heterobicycloalkyl ring system” refers to aheterobicycloalkyl with more than two common atoms.

Unless otherwise specified, positions occupied by hydrogen in theforegoing groups can be further substituted with substituentsexemplified by, but not limited to, hydroxy, oxo, nitro, methoxy,ethoxy, alkoxy, substituted alkoxy, trifluoromethoxy, haloalkoxy,fluoro, chloro, bromo, iodo, halo, methyl, ethyl, propyl, butyl, alkyl,alkenyl, alkynyl, substituted alkyl, trifluoromethyl, haloalkyl,hydroxyalkyl, alkoxyalkyl, thio, alkylthio, acyl, carboxy,alkoxycarbonyl, carboxamido, substituted carboxamido, alkylsulfonyl,alkylsulfinyl, alkylsulfonylamino, sulfonamido, substituted sulfonamido,cyano, amino, substituted amino, alkylamino, dialkylamino, aminoalkyl,acylamino, amidino, amidoximo, hydroxamoyl, phenyl, aryl, substitutedaryl, aryloxy, arylalkyl, arylalkenyl, arylalkynyl, pyridyl, imidazolyl,heteroaryl, substituted heteroaryl, heteroaryloxy, heteroarylalkyl,heteroarylalkenyl, heteroarylalkynyl, cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, cycloalkyl, cycloalkenyl, cycloalkylalkyl,substituted cycloalkyl, cycloalkyloxy, pyrrolidinyl, piperidinyl,morpholino, heterocycle, (heterocycle)oxy, and (heterocycle)alkyl; andpreferred heteroatoms are oxygen, nitrogen, and sulfur. It is understoodthat where open valences exist on these substituents they can be furthersubstituted with alkyl, cycloalkyl, aryl, heteroaryl, and/or heterocyclegroups, that where these open valences exist on carbon they can befurther substituted by halogen and by oxygen-, nitrogen-, orsulfur-bonded substituents, and where multiple such open valences exist,these groups can be joined to form a ring, either by direct formation ofa bond or by formation of bonds to a new heteroatom, preferably oxygen,nitrogen, or sulfur. It is further understood that the abovesubstitutions can be made provided that replacing the hydrogen with thesubstituent does not introduce unacceptable instability to the moleculesof the present invention, and is otherwise chemically reasonable.

“Optional” or “optionally” means that the subsequently described eventor circumstance may or may not occur, and that the description includesinstances where said event or circumstance occurs and instances in whichit does not. One of ordinary skill in the art would understand that withrespect to any molecule described as containing one or more optionalsubstituents, only sterically practical and/or synthetically feasiblecompounds are meant to be included. “Optionally substituted” refers toall subsequent modifiers in a term or series of chemical groups. Forexample, in the term “optionally substituted arylalkyl, the “alkyl”portion and the “aryl” portion of the molecule may or may not besubstituted, and for the series “optionally substituted alkyl,cylcoalkyl, aryl and heteroaryl,” the alkyl, cycloalkyl, aryl, andheteroaryl groups, independently of the others, may or may not besubstituted.

5.2 PROCESSES AND KETOREDUCTASE POLYPEPTIDES

Generally, enzymes belonging to the ketoreductase (KRED) or carbonylreductase class (EC1.1.1.184) are useful for the synthesis of opticallyactive alcohols from the corresponding prostereoisomeric ketonesubstrates and by stereoselective reduction of corresponding aldehydeand ketone substrates. KREDs typically convert a ketone or aldehydesubstrate to the corresponding alcohol product, but may also catalyzethe reverse reaction, oxidation of an alcohol substrate to thecorresponding ketone/aldehyde product. The reduction of ketones andaldehydes and the oxidation of alcohols by enzymes such as KRED use aco-factor, most commonly reduced nicotinamide adenine dinucleotide(NADH) or reduced nicotinamide adenine dinucleotide phosphate (NADPH),and nicotinamide adenine dinucleotide (NAD) or nicotinamide adeninedinucleotide phosphate (NADP+) for the oxidation reaction. NADH andNADPH serve as electron donors, while NAD+ and NADP+ serve as electronacceptors. KREDs and other alcohol dehydrogenases can accept either thephosphorylated or the non-phosphorylated co-factor (in its oxidized andreduced state).

In one aspect, the present disclosure relates to a process for theconversion of compound (2c) to compound (1c) in enantiomeric excess, asshown in Scheme 1 above, by using a ketoreductase derived fromLactobacillus.

In some embodiments, the process for preparing compound (1c) inenantiomeric excess,

comprises contacting compound (2c)

with a ketoreductase polypeptide from Lactobacillus, wherein theketoreductase is capable of converting compound (2c) to compound (1c) inenantiomeric excess, in presence of NADH or NADPH under suitablereaction conditions. In some embodiments, the ketoreductase is anon-naturally occurring ketoreductase derived from the ketoreductase ofSEQ ID NO:2, as further described below.

In some embodiments, any of the processes for the conversion of compound(2c) to compound (1c) can be carried out for conversion of a structuralanalog of compound (2c) with an engineered polypeptide of the presentdisclosure (e.g., as described in Table 3 and elsewhere herein) in thepresence of NADPH under suitable reaction conditions, thereby resultingin the preparation of the chiral alcohol of the corresponding analog ofproduct compound (1c) in enantiomeric excess. Suitable reactionconditions for the conversion of analogs of compound (2c) to the chiralalcohol of the corresponding analogs of compound (1c) can be the same asused for compound (2c) or determined by the ordinary artisan based onthe known properties of the analog compounds and routine experimentationin view of the guidance provided herein.

Accordingly, in some embodiments, the ketoreductases can be used toprepare in enantiomeric excess a chiral alcohol that is within the classof compounds represented by structural formula (1)

wherein

-   -   each ring A and B is independently an optionally substituted        monocyclic aryl or heteroaryl, R¹ is selected from hydrogen,        hydroxy, halo, cyano, carboxy, and an optionally substituted        alkyl, aminoalkyl, cycloalkyl, heterocycloalkyl,        alkyloxycarbonyl, aminocarbonyl, aminothiocarbonyl,        aminosulfonyl, and sulfonyl.

In some embodiments, R¹ is selected from H, —OH, —CN, —C(O)OR^(a),—(C1-C4)alkyl-NR^(b)R^(c), —C(O)NR^(b)R^(c), —C(S)NR^(b)R^(c),—SO₂NR^(b)R^(c), —SO₂R^(b), bicycloalkyl and heterobicycloalkyl, whereinR^(a), R^(b) and R^(c) are each independently selected from H and anoptionally substituted alkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, and heteroaryl. Exemplary R¹ groups include,among others, —C(O)NH₂, dimethylaminopropyl, methylaminopropyl, andquinuclidinyl.

In some embodiments, the aryl or heteroaryl groups for rings A and B areselected from optionally substituted phenyl, pyridyl, or thienyl.Optional substituents on rings A and B include, but are not limited to—²H, —OH, —SH, halo, and optionally substituted alkyl, alkenyl, alkynyl,aryl, heteroaryl, alkoxy, and amino groups. Optional substituents on R¹groups, where applicable, include but are not limited to, alkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, and heteroarylgroups, which may be further optionally substituted. Compounds ofstructural formula (1) encompass structural analogs of compound (1c).

Thus, in some embodiments, the process for preparing a compound ofstructural formula (1) in enantiomeric excess, comprises contacting acompound of structural formula (2)

wherein rings A and B, and R¹ are defined above, with any of theketoreductases described herein, wherein the ketoreductase is capable ofconverting compound (2) to compound (1) in enantiomeric excess, inpresence of NADH or NADPH under suitable reaction conditions.

In some embodiments, the ketoreductases can be used to prepare inenantiomeric excess a chiral alcohol of the class of compoundsrepresented by structural formula (1a),

wherein

R¹ is selected from hydrogen, hydroxy, halo, cyano, carboxy, and anoptionally substituted alkyl, aminoalkyl, cycloalkyl, heterocycloalkyl,alkyloxycarbonyl, aminocarbonyl, aminothiocarbonyl, aminosulfonyl, andsulfonyl.

In some embodiments, R¹ of structural formula (1a) is selected from —OH,—CN, —C(O)OR^(a), —(C1-C4)alkyl-NR^(b)R^(c), —C(O)NR^(b)R^(c),—C(S)NR^(b)R^(c), —SO₂NR^(b)R^(c), —SO₂R^(b), bicycloalkyl andheterobicycloalkyl, wherein R^(a), R^(b) and R^(c) are eachindependently selected from H and an optionally substituted alkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl.

Accordingly, in some embodiments, the process for preparing a compoundof structural formula (1a) in enantiomeric excess, comprises contactinga compound of structural formula (2a)

wherein

R¹ is defined above, with any of the ketoreductases described herein,wherein the ketoreductase is capable of converting compound (2a) tocompound (1a) in enantiomeric excess, in presence of NADH or NADPH undersuitable reaction conditions.

In some embodiments, a structural analog of compound (1c) is representedby structural formula (1b);

wherein

R² is selected from —OH, —C(O)OR^(d), —C(O)NH₂, —CN,dimethylaminopropyl, methylaminopropyl, and quinuclidinyl, where R^(d)is (C1-C4) alkyl.

Thus, in some embodiments, the process for preparing a compound ofstructural formula (1b) in enantiomeric excess, comprises contacting acompound of structural formula (2b)

wherein R² is defined above, with any of the ketoreductases describedherein, wherein the ketoreductase is capable of converting compound (2b)to compound (1b) in enantiomeric excess, in presence of NADH or NADPHunder suitable reaction conditions.

In some embodiments, the R² group for the compound of structural formula(2b) is —CN, such that the process results in the preparation of anenantiomeric excess of compound (1d)

While the processes using the ketoreductase can be used to directlyconvert compound (2c) to compound (1c), compound (1d) can also be usedto prepare compound (1c) as shown in Scheme 2:

Accordingly, the present disclosure also provides a process forpreparing compound (1c) in enantiomeric excess by contacting compound(2d) with a ketoreductase under suitable reactions to form compound (1d)in enantiomeric excess; and converting compound (1d) to compound (1c).The conversion of compound (1d) to compound (1c) can use conventionaltechniques, such as hydrolysis of the cyano group to the amide (see,e.g., U.S. Pat. No. 4,008,241 and U.S. Pat. No. 4,629,700).

In some embodiments, the R² group for the compound of structural formula(2b) is—dimethylaminopropyl or methylaminopropyl, such that the processresults in preparation of an enantiomeric excess of compound (1e)

where R^(e) is H or methyl. Accordingly, in some embodiments, a processfor preparing compound (1e) in enantiomeric excess comprises contactingcompound (2e)

where R^(e) is defined above, with any of the ketoreductases describedherein, wherein the ketoreductase is capable of converting compound (2e)to compound (1e) in enantiomeric excess, in presence of NADH or NADPHunder suitable reaction conditions.

In some embodiments, the R² group for the compound of structural formula(2b) is—quinuclidinyl such that the process results in the preparationof an enantiomeric excess of compound (1f)

Accordingly, in some embodiments, a process for preparing compound (1f)in enantiomeric excess comprises contacting compound (2f)

with any of the ketoreductases described herein, wherein theketoreductase is capable of converting compound (2f) to compound (1f) inenantiomeric excess, in presence of NADH or NADPH under suitablereaction conditions. As will be apparent to the person of ordinary skillin the art, compound (1f) and compound (1e) are metabolites ofImipramine and Quinupramine, respectively (see, e.g., Chen et al., 1997,J Chromatogr B Biomed Sci Appl. 693(1):153-8; Nielsen et al., 1993, JChromatogr. 612(1):87-95), which are tricyclic antidepressants used fortreatment of depression and enuresis. Imipramine and Quinupramine havethe following structures:

In some embodiments, the process for the conversion of a structuralanalog of compound (2c) to the corresponding chiral alcohol can becarried out, wherein the analog of compound (2c) is a deuterated versionof the compound (2c) (i.e., a molecule having the same structure ascompound (2c) but with one or more the hydrogen atoms of compound (2c)substituted with a deuterium atom) (see, e.g., U.S. Pat. No. 7,705,036B2). Similarly, the processes for the conversion of an analog ofcompound (2c) to an analog of compound (1c) can be carried out with thedeuterated version of any of the above described compounds of formula(2), compounds of formula (2a), compounds of formula (2b), compounds offormula (2d), compounds of formula (2e), and compounds of formula (2f)described above.

As noted herein, the process for conversion of the prostereoisomericketone to the corresponding chiral alcohol uses a ketoreductase fromLactobacillus. In some embodiments, the ketoreductase comprises anon-naturally occurring, engineered polypeptide with improved enzymaticproperties for the conversion of compound (2c) or a structural analogthereof to compound (1c) or the corresponding structural analog,relative to the naturally occurring ketoreductase polypeptide of SEQ IDNO: 2, including, among others, increased conversion rates, highstereoselectivity, increased solvent stability, and increased thermalstability.

In some embodiments, the non-naturally occurring, engineeredketoreductase polypeptides disclosed herein are capable of carrying outthe conversion with high enantiomeric excess (e.g., at least about 99%e.e.), increased activity (e.g., at least about 10-fold increasedactivity relative to the reference polypeptide SEQ ID NO:4 or 6), highpercent conversion (e.g., at least about 90% conversion in 24 h), in thepresence of high substrate loadings (e.g., at least about 50 g/L to 100g/L of compound (2c)).

In some embodiments of the process, the ketoreductase capable ofconverting compound (2c) or structural analog thereof to compound (1c)or corresponding structural analog in enantiomeric excess comprises anamino acid sequence that has at least 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to areference polypeptide selected from SEQ ID NO: 6, 8, 10, 12, 14, 16, 18,20, 22, 24, 26, 28, 30, 32, 34, 36, and 38, as further described below.

In some embodiments, the ketoreductase is a non-naturally occurringketoreductase polypeptide comprising an amino acid sequence that has atleast 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% sequence identity to the reference polypeptide of SEQID NO:10.

In some embodiments, the ketoreductase is a non-naturally occurringketoreductase polypeptide comprising an amino acid sequence that has atleast 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% sequence identity to the reference polypeptide of SEQID NO:16.

In some embodiments, the ketoreductase is a non-naturally occurringketoreductase polypeptide comprising an amino acid sequence that has atleast 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% sequence identity to a reference polypeptide of SEQ IDNO:36.

Exemplary embodiments of ketoreductases that can be used in the processare disclosed in more detail below, including the ketoreductasepolypeptides disclosed in Table 3, and it is to be understood that anyof the ketoreductases disclosed herein is applicable to any of theprocess described in this section.

In the present disclosure, the processes are carried out under suitablereaction conditions, and contemplate ranges of suitable reactionconditions that can be used in the conversion reactions. These include,but are not limited to, ranges of polypeptide loading, conditions withthe polypeptide immobilized on a solid support, substrate loading,cofactor loading, pH, temperature, buffer, solvent system, atmosphericpressure, and reaction time. The present disclosure also contemplatesthat the methods comprising the biocatalytic conversion described aboveusing an engineered polypeptide of the disclosure can further comprisechemical steps of compound (1c) product, or corresponding structuralanalog work-up, extraction, isolation, purification, and/orcrystallization, each of which can be carried out under a range ofconditions.

In the processes herein, the ketoreductase is used in an amount capableof producing the desired amount of product, e.g., compound (1c), ordesired percent conversion of substrate to product under the reactioncondition used. As will be apparent to the skilled artisan, non-natural,engineered ketoreductases with increased enzymatic activity and higherpercentage conversion efficiency allows the use of lower concentrationsof the engineered polypeptide. The use of lower concentration ofengineered polypeptide in turn reduces the amount of residual proteinthat may need to be removed in subsequent steps for purification of theproduct compound. In some embodiments, the processes of the presentdisclosure can be carried out wherein the reaction conditions comprisean engineered polypeptide concentration of about 0.1 g/L to about 10g/L, about 0.1 g/L to about 5 g/L, about 0.1 g/L to about 2 g/L, orabout 0.1 g/L to about 1.0 g/L. In some embodiments, the ketoreductasepolypeptide concentration is at about 10 g/L, about 5 g/L, about 4 g/L,about 2 g/L, about 1 g/L, about 0.5 g/L, about 0.2 g/L or about 0.1 g/L.In some embodiments, the reaction conditions for the biocatalyticconversion processes disclosed herein, include conditions wherein theketoreductase polypeptide is immobilized on a solid support. Suchimmobilization can allow for reuse of the polypeptide.

In some embodiments, the processes can be carried out under reactionconditions comprising a compound (2c) loading of about 1 g/L to about400 g/L, about 10 g/L to about 400 g/L, about 20 g/L to about 400 g/L,about 40 g/L to about 400 g/L, about 50 g/L to about 400 g/L. about 75g/L to about 400 g/L, about 100 g/L to about 400 g/L, about 125 g/L toabout 400 g/L, about 150 g/L to about 400 g/L, about 175 g/L to about400 g/L, about 200 g/L to about 400 g/L, or even greater. In someembodiments, the reaction conditions comprise a compound (2c) loading ofabout 1 g/L to about 200 g/L, about 10 g/L to about 200 g/L, about 20g/L to about 200 g/L, about 40 g/L to about 200 g/L, about 50 g/L toabout 200 g/L. about 75 g/L to about 200 g/L, about 100 g/L to about 200g/L, or about 50 g/L to about 150 g/L. In some embodiments, the reactionconditions comprise a compound (2c) loading of about 1 g/L, about 10g/L, about 20 g/L, about 40 g/L, about 50 g/L, about 75 g/L, about 100g/L, about 125 g/L, about 150 g/L, about 175 g/L, about 200 g/L, about300 g/L, or about 400 g/L. While the values for substrate loadingsprovided herein are based on the molecular weight of compound (2c), italso is contemplated that the equivalent molar amounts of varioushydrates and salts of compound (2c) as well as structural analogs, e.g.,compounds encompassed by structural formula (2), structural formula(2a), structural formula (2b), structural formula (2d), structuralformula (2e) and structural formula (2f), also can be used in theprocesses. The substrate loading used in the processes herein can takeinto account, among others, substrate solubility in the reactionsolvent, tolerability of the biocatalyst to the substrate loading, andthe percent conversion under the reaction conditions used.

In the embodiments herein, the reaction conditions comprise atemperature suitable for activity of the biocatalyst and desiredconversion of substrate to product. In some embodiments, the use ofengineered polypeptides having increased thermal stability relative tothe naturally occurring ketoreductase polypeptide of SEQ ID NO: 2 allowsthe processes, e.g., conversion of compound (2c) to compound (1c), to becarried out at higher temperatures, which can result in increasedconversion rates and improved substrate solubility characteristics. Oneof skill in the art can assess the advantages of carrying out thereaction at a higher temperature and the potential disadvantages ofproduct degradation and enzyme inactivation at the higher temperatures.In some embodiments, the processes can be carried out under reactionconditions comprising a temperature of about 20° C. to about 60° C.,about 25° C. to about 60° C., about 30° C. to about 60° C., about 35° C.to about 60° C., about 40° C. to about 60° C., about 45° C. to about 60°C., about 45° C. to about 55° C., or about 50° C. to about 55° C. Insome embodiments, the temperature during the enzymatic reaction can bemaintained at ambient (e.g., 25° C.), 27° C., 30° C., 32° C., 35° C.,37° C., 40° C.; 45° C., 50° C., 55° C. or 60° C. or in some embodimentsadjusted over a temperature profile during the course of the reaction.

In some embodiments, the processes herein for preparing compound (1c)and structural analogs thereof are carried out under reaction conditionsat a desired pH or within a desired pH range by the addition of an acidor a base. In some embodiments, this may be done during the course ofthe reaction. In some embodiments, the pH of the reaction mixture maychange or be changed during the course of the reaction. Thus, in someembodiments the pH may be controlled by using an aqueous solvent thatcomprises a buffer. Suitable buffers to maintain desired pH ranges areknown in the art and include, but are not limited to, phosphate buffer,triethanolamine (TEA) buffer, and the like. Combinations of bufferingand acid or base addition may also be used.

In some embodiments, the processes for preparing compound (1c) orstructural analogs thereof can be carried out under reaction conditionscomprising a pH of about 6 to about 12, a pH or about 6 to about 11, apH of about 7 to about 11, a pH of about 7 to about 10, a pH of about 8to about 10, a pH of about 9 to about 10, a pH of about 8 to about 9.5,or a pH of about 8 to about 9. In some embodiments, the reactionconditions comprise a pH of about 6, a pH of about 6.5, a pH of about 7,a pH of about 7.5, a pH of about 8, a pH of about 8.5, a pH of about 9,a pH of about 9.5, a pH of about 10, a pH of about 10.5, a pH of about11, a pH of about 11.5 or a pH of about 12. A person of ordinary skillin the art can use an appropriate pH or a range of pH by considering, byway of example and not limitation, stability and activity of theketoreductase, stability of substrate and product, and stability of thecofactor.

Generally, the processes of the present disclosure are carried out in asolvent. Suitable solvents include water, aqueous buffer solutions,organic solvents, and/or co-solvent systems, which generally compriseaqueous solvents and organic solvents.

In some embodiments, the processes can be carried out under reactionconditions comprising an aqueous buffer solution, an organic solvent, ora co-solvent system. In some embodiments, the buffer solution isselected from TEA, for example, of about 0.025 M to about 0.25 M TEA,and potassium phosphate, for example, about 0.025 M to about 0.25 Mphosphate. In some embodiments, the co-solvent system comprises about95% (v/v) to about 5% (v/v) of an aqueous buffer solution (e.g., about0.1 M TEA), and about 5% (v/v) to about 95% (v/v) of an organic solventsolution (e.g., IPA). In some embodiments, the co-solvent systemcomprises about 30% (v/v) to about 70% (v/v) of an aqueous buffersolution (e.g., about 0.1 M TEA) and about 70% (v/v) to about 30% (v/v)of an organic solvent solution (e.g., IPA). In some embodiments, thereaction conditions comprise water as a suitable solvent with no bufferpresent.

In some embodiments, the co-solvent system comprises an aqueous buffersolution and IPA, wherein the IPA concentration is about 5% (v/v) toabout 95% (v/v), about 10% (v/v) to about 90%, (v/v) about 15% (v/v) toabout 90% (v/v), about 20% (v/v) to about 90% (v/v), about 25% (v/v) toabout 80% (v/v), about 25% (v/v) to about 75% (v/v), about 35% (v/v) toabout 75% (v/v), about 45% (v/v) to about 75% (v/v), about 55% (v/v) toabout 75% (v/v), about 60% (v/v) to about 70% (v/v), or about 60% (v/v)to about 65% (v/v). In some embodiments, the IPA concentration is atleast about 25% (v/v), at least about 35% (v/v), at least about 45%(v/v), at least about 55% (v/v), about 60% (v/v), about 65% (v/v), about70% (v/v), about 75% (v/v), about 80%, about 85% (v/v), about 90% (v/v)or about 95% (v/v). In some embodiments, the reaction conditionscomprise a co-solvent system of 0.1 M TEA buffer and about 60% (v/v) toabout 70% (v/v) IPA. In some embodiments, the reaction conditionscomprise a co-solvent system of about 0.1 M TEA buffer and about 95%(v/v), about 0.1 M TEA buffer and about 90% (v/v) IPA, about 0.1 M TEAbuffer and about 85% (v/v) IPA, about 0.1 M TEA buffer and about 80%(v/v) IPA, about 0.1 M TEA buffer and about 75% (v/v) IPA, about 0.1 MTEA buffer and about 70% (v/v) IPA, about 0.1 M TEA buffer and about 65%(v/v) IPA, about 0.1 M TEA buffer and about 65% (v/v) IPA, or about 0.1M TEA buffer and about 60% (v/v) IPA.

Generally, in the processes of the present disclosure, an electron donoris used in the reduction reaction carried out by the ketoreductase. Insome embodiments, the electron donor is a cofactor. Suitable cofactorsinclude, but are not limited to, NADP⁺ (nicotinamide adeninedinucleotide phosphate), NADPH (the reduced form of NADP⁺), NAD⁺(nicotinamide adenine dinucleotide) and NADH (the reduced form of NAD⁺).Generally, the reduced form of the cofactor is added to the reactionmixture. Accordingly, in some embodiments, the processes are carried outin presence of an electron donor selected from NADPH cofactor or NADHcofactor. In some embodiments, the electron donor is NADPH cofactor. Insome embodiments, the process can be carried out wherein the reactionconditions comprise an NADH or NADPH cofactor concentration of about0.03 to about 1 g/L, 0.03 to about 0.8 g/L, about 0.03 to about 0.5 g/L,about 0.05 to about 0.3 g/L, about 0.05 to about 0.2 g/L, or about 0.1to about 0.2 g/L. In some embodiments, the process is carried out underNADH or NADPH cofactor concentration of about 1 g/L, about 0.8 g/L,about 0.5 g/L, about 0.3 g/L, about 0.2 g/L, about 0.1 g/L, about 0.05g/L, or about 0.03 g/L.

In some embodiments of the process, an optional cofactor recyclingsystem, also referred to as a cofactor regeneration system, can be usedto regenerate cofactor NADPH/NADH from NADP+/NAD+ produced in theenzymatic reaction. A cofactor regeneration system refers to a set ofreactants that participate in a reaction that reduces the oxidized formof the cofactor (e.g., NADP⁺ to NADPH). Cofactors oxidized by thepolypeptide reduction of the keto substrate are regenerated in reducedform by the cofactor regeneration system. Cofactor regeneration systemscomprise a stoichiometric reductant that is a source of reducinghydrogen equivalents and is capable of reducing the oxidized form of thecofactor. The cofactor regeneration system may further comprise acatalyst, for example an enzyme catalyst, that catalyzes the reductionof the oxidized form of the cofactor by the reductant. Cofactorregeneration systems to regenerate NADH or NADPH from NAD⁺ or NADP⁺,respectively, are known in the art and can be used in the methodsdescribed herein.

Suitable exemplary cofactor regeneration systems that may be employedinclude, but are not limited to, glucose and glucose dehydrogenase,formate and formate dehydrogenase, glucose-6-phosphate andglucose-6-phosphate dehydrogenase, a secondary (e.g., isopropanol)alcohol and secondary alcohol dehydrogenase, phosphite and phosphitedehydrogenase, molecular hydrogen and hydrogenase, and the like. Thesesystems may be used in combination with either NADP⁺/NADPH or NAD⁺/NADHas the cofactor. Electrochemical regeneration using hydrogenase may alsobe used as a cofactor regeneration system. See, e.g., U.S. Pat. Nos.5,538,867 and 6,495,023, both of which are incorporated herein byreference. Chemical cofactor regeneration systems comprising a metalcatalyst and a reducing agent (for example, molecular hydrogen orformate) may also be suitable. See, e.g., PCT publication WO2000/053731, which is incorporated herein by reference.

In some embodiments, the cofactor recycling system comprises glucosedehydrogenase (GDH), which is a NAD⁺ or NADP⁺-dependent enzyme thatcatalyzes the conversion of D-glucose and NAD⁺ or NADP⁺ to gluconic acidand NADH or NADPH, respectively. Glucose dehydrogenases suitable for usein the practice of the processes described herein include naturallyoccurring glucose dehydrogenases as well as non-naturally occurringglucose dehydrogenases. Naturally occurring glucose dehydrogenaseencoding genes have been reported in the literature, e.g., the Bacillussubtilis 61297 GDH gene, B. cereus ATCC 14579 and B. megaterium.Non-naturally occurring glucose dehydrogenases generated using, forexample, mutagenesis, directed evolution, and the like and are providedin PCT publication WO 2005/018579, and US publication Nos. 2005/0095619and 2005/0153417. All of these sequences are incorporated herein byreference.

In some embodiments, the co-factor regenerating system comprises aformate dehydrogenase, which is a NAD⁺ or NADP⁺-dependent enzyme thatcatalyzes the conversion of formate and NAD⁺ or NADP⁺ to carbon dioxideand NADH or NADPH, respectively. Formate dehydrogenases suitable for useas cofactor regenerating systems in the ketoreductase reactionsdescribed herein include naturally occurring and non-naturally occurringformate dehydrogenases. Suitable formate dehydrogenases are described inPCT publication WO 2005/018579, incorporated herein by reference.Formate may be provided in the form of a salt, typically an alkali orammonium salt (for example, HCO₂Na, KHCO₂NH₄, and the like), in the formof formic acid, typically aqueous formic acid, or mixtures thereof. Abase or buffer may be used to provide the desired pH.

In some embodiments, the co-factor regenerating system comprises asecondary alcohol dehydrogenase, which is an NAD⁺ or NADP⁺-dependentenzyme that catalyzes the conversion of a secondary alcohol and NAD⁺ orNADP⁺ to a ketone and NADH or NADPH, respectively. Secondary alcoholdehydrogenases suitable for use as cofactor regenerating systems in theprocesses described herein include naturally occurring and non-naturallyoccurring ketoreductases. Naturally occurring secondary alcoholdehydrogenases include known alcohol dehydrogenases from, by way ofexample and not limitation, Thermoanerobium brockii, Rhodococcuserythropolis, Lactobacillus kefir, and Lactobacillus brevis, andnon-naturally occurring secondary alcohol dehydrogenases includeengineered alcohol dehydrogenases derived therefrom. In someembodiments, non-naturally occurring ketoreductases engineered forthermo- and solvent stability can be used. Such ketoreductases aredescribed in the present application and the patent publications US20080318295A1; US 20090093031A1; US 20090155863A1; US 20090162909A1; US20090191605A1; US 20100055751A1; WO/2010/025238A2; WO/2010/025287A2; andUS 20100062499A1; each of which are incorporated by reference herein.

As will be apparent from this disclosure, the engineered ketoreductasepolypeptides described herein are capable of converting IPA to acetoneto regenerate the cofactor NADH/NADPH for NAD+/NADP+, respectively.Thus, in some embodiments of the processes for carrying out theconversion of compound (2c) or structural analogs thereof to compound(1c) or its corresponding structural analogs, the ketoreductase of thecofactor regeneration system is the engineered ketoreductasepolypeptides of present disclosure, and used with a secondary alcohol asa reductant to recycle the NADPH or NADH cofactor in the reactionmixture.

Suitable secondary alcohols useful in cofactor regenerating systemsinclude lower secondary alkanols and aryl-alkyl carbinols. Exemplarylower secondary alcohols include, but are not limited to, isopropanol,2-butanol, 3-methyl-2-butanol, 2-pentanol, 3-pentanol,3,3-dimethyl-2-butanol, and the like. In some embodiments, the secondaryalcohol is isopropanol (IPA). Suitable aryl-alkyl carbinols includeunsubstituted and substituted 1-arylethanols.

In some embodiments, the processes can be carried out without addingNADPH or NADH cofactor during the reaction and without any other enzymesystems present (e.g., glucose dehydrogenase, or formate dehydrogenase).

In some embodiments, the processes of the disclosure can be carried outwherein no cofactor recycling enzyme is present other than theengineered polypeptide. For example, the reaction conditions cancomprise an IPA concentration of about 55-75% (v/v), an NADPH or NADHcofactor loading of about 0.03-0.5 g/L, and wherein no cofactorrecycling enzyme is present other than the engineered ketoreductasepolypeptide.

In some embodiments where the cofactor recycling system produces avolatile product, such as acetone from isopropanol, the volatile productcan be removed by sparging the reaction solution with a non-reactive gasor by applying a vacuum to lower the reaction pressure and removing thevolatile present in the gas phase. A non-reactive gas is any gas thatdoes not react with the reaction components. Various non-reactive gasesinclude nitrogen and noble gases (e.g., inert gases). In someembodiments, the non-reactive gas is nitrogen gas. For example, acetoneformed by oxidation of isopropanol can be removed by sparging thereaction solution with nitrogen gas or applying a vacuum to the reactionsolution and removing the acetone from the gas phase by an acetone trap,such as a condenser or other cold trap.

In the embodiments herein, the polypeptides carrying out the conversionof compound (2c) or structural analog thereof to compound (1c) orcorresponding structural analog, and any additional enzymes of theoptional cofactor regeneration system, may be added to the reactionmixture in the form of the purified enzymes, whole cells transformedwith gene(s) encoding the enzymes, and/or cell extracts and/or lysatesof such cells.

In some embodiments, the gene(s) encoding the ketoreductase polypeptidesand the optional cofactor regeneration enzymes can be transformed intohost cells separately or together into the same host cell for expressionof the enzymes. Whole cells transformed with gene(s) encoding theengineered ketoreductase enzyme and/or the optional cofactorregeneration enzymes, or cell extracts and/or lysates thereof, may beemployed in a variety of different forms, including solid (e.g.,lyophilized, spray-dried, and the like) or semisolid (e.g., a crudepaste). In some embodiments, the transformed cells, cell extracts,lysates, or isolated enzyme, can be immobilized on a solid support andthe conversion reactions carried by contacting the solid support withthe substrate compound.

Generally, the order of addition of reactants (e.g., substrate,cofactor, polypeptide, etc.) is not critical to the processes of thepresent disclosure. The reactants may be added together at the same timeto a solvent (e.g., monophasic solvent, biphasic aqueous co-solventsystem, and the like), or alternatively, some of the reactants may beadded separately, and some together at different time points.

In some embodiments, the process for preparing the compound (1c) orstructural analogs thereof can be carried out using any combination of amixture and reaction conditions disclosed above or elsewhere herein.Accordingly, in some embodiments, the processes described hereincomprise the following reaction condition: (a) the ketoreductasepolypeptide is at about 0.1 g/L to about 1 g/L; (b) compound (2c) is ata loading of about 100 g/L to about 200/g/L; (c) NADP(H) is about 0.1g/L to about 0.01 g/L; (d) a co-solvent solution of an aqueous buffer,and IPA of about 50% to about 70% (v/v), and (e) a temperature of about45° C. to about 60° C.

In some embodiments, the processes described herein comprise thefollowing reaction conditions: (a) the ketoreductase polypeptide is atabout 1 g/L to about 3 g/L; (b) compound (2c) is at a loadingconcentration of about 50 g/L to about 175 g/L; (c) NADP(H) is about 0.1g/L to about 0.5 g/L; (d) a co-solvent solution of an aqueous buffer andIPA of about 50% to about 70% (v/v), and (e) a temperature of about 45°C. to about 60° C.

In some embodiments, the processes described herein comprise thefollowing reaction conditions: (a) the ketoreductase polypeptide is atabout 1 g/L to about 3 g/L to about 10 g/L; (b) compound 2(c) is at aloading concentration of about 50 g/L to about 175 g/L; (c) NADP(H) isabout 0.5 g/L to about 1 g/L; (d) a co-solvent solution of an aqueousbuffer and IPA of about 50% to about 70% (v/v), and (e) a temperature ofabout 45° C. to about 60° C.

In some embodiments, in the process for the conversion of compound (2c)to compound (1c), compound (2c) is at a loading of about 50 g/L to about200 g/L and the process results in at least about 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99% or greater conversion of compound (2c) tocompound (1c) in 24 h or less.

In some embodiments, in the process for the conversion of compound (2c)to compound (1c), compound (2c) is at a loading of about 50 g/L to about200 g/L and the process results in enantiomeric excess of at least about91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater of compound (1c)in 24 h or less.

As noted throughout this disclosure, eslicarbazepine acetate is theprodrug form of eslicarbazepine (i.e., compound (1c)). Upon oraladministration, eslicarbazepine acetate is efficiently absorbed in thegastrointestinal tract and metabolized to eslicarbazepine. Hence, theprocesses described herein for efficient synthesis of eslicarbazepinealso provides an improved method for preparation of eslicarbazepineacetate and its structural analogs.

Accordingly, in some embodiments, a method for preparing compound (3) orstructural analog thereof in enantiomeric excess,

wherein,

rings A and B are as defined for structural formula (1) above;

R¹ is selected from hydrogen, hydroxy, halo, cyano, carboxy, and anoptionally substituted alkyl, aminoalkyl, cycloalkyl, heterocycloalkyl,alkyloxycarbonyl, aminocarbonyl, aminothiocarbonyl, aminosulfonyl, andsulfonyl; and

R³ is a hydroxyl protecting group or —C(O)R⁴, wherein R⁴ is selectedfrom H, alkyl, aminoalkyl, haloalkyl, aralkyl, cycloalkyl,cycloalkylalkyl, alkoxy, aryl, substituted phenyl or pyridyl, comprisesa step of converting compound (2) to compound (1) by any of theprocesses described herein for preparing compound (1).

As noted above, in some embodiments, R¹ of structural formula (3) can beselected from —OH, —CN, —C(O)OR^(a), —(C1-C4)alkyl-NR^(b)R^(c),—C(O)NR^(b)R^(c), —C(S)NR^(b)R^(c), —SO₂NR^(b)R^(c), —SO₂R^(b),bicycloalkyl, and heterobicycloalkyl, wherein R^(a), R^(b) and R^(c) areeach independently selected from H and an optionally substituted alkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl.

A protecting group when attached to a reactive functional group in amolecule, masks, reduces or prevents the reactivity of the functionalgroup. Examples of hydroxyl protecting groups can be found in Greene andWuts, Protective Groups in Organic Chemistry, 3rd Ed., 1999, John Wiley& Sons, NY and Harrison et al., Compendium of Synthetic Organic Methods,Vols. 1-8, 1971-1996, John Wiley & Sons, NY. Representative hydroxylprotecting groups include, but are not limited to, lower alkyl groups(for example tert-butyl), lower alkenyl groups (for example allyl);lower alkanoyl groups (for example acetyl); lower alkoxycarbonyl groups(for example tert-butoxycarbonyl); lower alkenyloxycarbonyl groups (forexample allyloxycarbonyl); aryl lower alkoxycarbonyl groups (for examplebenzoyloxycarbonyl, p-methoxybenzyloxycarbonyl,o-nitrobenzyloxycarbonyl, p-nitrobenzyloxycarbonyl); tri loweralkylsilyl (for example trimethylsilyl, tert-butyldimethylsilyl) andaryl lower alkyl (for example benzyl) groups.

In some embodiments, a method for preparing compound (4) or structuralanalog thereof in enantiomeric excess,

wherein

R¹ is as defined above; and

R⁴ is selected from H, alkyl, aminoalkyl, haloalkyl, aralkyl,cycloalkyl, cycloalkylalkyl, alkoxy, aryl, particularly an optionallysubstituted phenyl or pyridyl,

comprises a step of converting compound (2a) to compound (1a) by any ofthe processes described herein for preparing compound (1a).

In some embodiments, a method for preparing compound (5) or structuralanalog thereof in enantiomeric excess,

wherein

R² is selected from —OH, —C(O)OR^(d), —C(O)NH₂, —CN,dimethylaminopropyl, methylaminopropyl, and quinuclidinyl, where R^(d)is (C1-C4) alkyl; and

R⁴ is selected from H, alkyl, aminoalkyl, haloalkyl, aralkyl,cycloalkyl, cycloalkylalkyl, alkoxy, aryl, particularly an optionallysubstituted phenyl or pyridyl;

comprises a step of converting compound (2b) to compound (1b) by any ofthe processes described herein for preparing compound (1b).

In some embodiments, a method for preparing compound (6) in enantiomericexcess,

wherein

R⁴ is selected from H, alkyl, aminoalkyl, haloalkyl, aralkyl,cycloalkyl, cycloalkylalkyl, alkoxy, aryl, particularly an optionallysubstituted phenyl or pyridyl;

comprises a step of converting compound (2c) to compound (1c) inenantiomeric excess by any of the processes described above forpreparing compound (1c).

In some embodiments, a method for preparing compound (6) in enantiomericexcess, wherein R⁴ is methyl (i.e., compound (6a)),

comprises a step of converting compound (2c) to compound (1c) inenantiomeric excess by any of the processes described herein forpreparing compound (1c) in enantiomeric excess.

In some embodiments, the method for preparing compound (6a) inenantiomeric excess can further comprise a step of converting compound(1c) to compound (6a). In some embodiments, preparing compound (6a) fromcompound (1c) is by use of an acylating agent (see, e.g., U.S. Pat. No.5,753,646, incorporated herein by reference).

In the processes of the present disclosure, the conversion reactions aremediated by ketoreductases from Lactobacillus. In some embodiments, theketoreductases are non-natural, engineered ketoreductases that haveresidue differences as compared to the naturally occurring ketoreductaseof L. kefir represented by SEQ ID NO:2. These differences occur atresidue positions that can affect enzyme activity, stereoselectivity,thermostability, solvent stability, polypeptide expression, co-factoraffinity, or various combinations thereof. Table 2 provides acorrelation of amino acid residue positions and the associated role inenzyme properties.

TABLE 2 Structural locations useful for engineered ketoreductasepolypeptides Position Structural location Associated functionalproperties X17 NADPH-Binding Site Activity/Thermostability X21 SurfaceThermostability X25 Surface Thermostability/Solvent stability X29Surface Thermostability/Solvent stability X40 NADPH-Binding Site Tightbinding of NADPH to enzyme X43 Surface Thermostability X64 NADPH-BindingSite Interacts with NADPH Adenine ring X71 SurfaceThermostability/Solvent stability X76 Surface Solvent stability X80Surface Solvent stability X87 Tetramer interfaceActivity/Thermostability/Solvent stability X93 Second sphere active siteThermostability X94 Second sphere active site Thermostability X95 Secondsphere active site Activity/Thermostability/Solvent Stability X96 Secondsphere active site Activity/Thermostability/Solvent Stability X99Dimer-tetramer interface Thermostability/Solvent stability X108Dimer-tetramer interface Thermostability/Solvent stability X117 CoreThermostability/Solvent stability X127 Second sphere active siteThermostability/Solvent stability X131 Surface Activity/ThermostabilityX144 Active site Activity X145 Active site Activity X147 Dimer-tetramerActivity/Thermostability/Solvent interface/core stability X148Dimer-tetramer interface Thermostability/Solvent stability X150 Activesite Activity X152 Second sphere active site Activity X153 Second sphereactive site Activity X155 Position interacting Activity with 95 X157Core Activity/Thermostability/Solvent Stability X173 Dimer interfaceActivity/Thermostability/Solvent Stability X190 Active site ActivityX194 Surface Activity X195 Second sphere active site ThermostabilityX196 Active site Activity X199 Active site Activity X200 SurfaceThermostability X201 Active site Activity X202 Flexible loop ActivityX203 Flexible loop Activity X204 Flexible loop Activity X205 Flexibleloop Activity X206 Flexible loop Activity X207 Flexible loop ActivityX211 Second sphere active site Activity X221 SurfaceThermostability/Solvent stability X223 Core Thermostability/Solventstability X226 Dimer-tetramer interface Thermostability/Solventstability X233 Surface Activity X249 Active site Activity

The structure-function information was obtained by identifyingengineered ketoreductases active in the conversion of compound (2c) tocompound (1c), where the identified ketoreductases have various residuedifferences from the reference polypeptide of SEQ ID NO:2 and displayedcertain desirable properties, including among others, desirable changesin enzyme activity, stereoselectivity, thermostability, solventstability, co-factor affinity, polypeptide expression, or variouscombinations thereof. The odd numbered sequence identifiers (i.e., SEQID NOs) refer to the nucleotide sequence encoding the amino acidsequence provided by the even numbered SEQ ID NOs, and the sequences areprovided in the electronic Sequence Listing file accompanying thisdisclosure, which is hereby incorporated by reference herein. The aminoacid residue differences are based on comparison to the referencesequence of SEQ ID NO: 2. The activity of each engineered polypeptiderelative to the reference polypeptide of SEQ ID NO: 4 was determined asconversion of substrate of compound (2c) to product of compound (1c)over a 24 h period at room temperature in a high-throughput (HTP)96-well plate format assay of cell lysates containing the engineeredpolypeptides. General HTP assay protocol and reaction conditions were asfollows: a total 200 μL reaction volume in a deep-well 96-well platescontaining 10 μL of polypeptide clear lysate, 0.05 g/L NADP+, 70%isopropyl alcohol (IPA), 0% to 1% acetone, 5.0 g/L to 100 g/L substrate,and 0% to 5% DMSO. Specific modifications of the HTP assay protocols atdifferent rounds of evolution are as noted in Table 3. Additional assayprotocols and experimental details useful for determining engineeredpolypeptide activities are provided in the Examples. The levels ofactivity (i.e., “+” “++” “+++” etc.) are defined as follows: “+”indicates at least equal to but less than 2 times the activity of SEQ IDNO: 4; “++” indicates at least 2 times but less than 10 times theactivity of SEQ ID NO: 4; “+++” indicates at least 10 times but lessthan 25 times the activity of SEQ ID NO: 4; “++++” indicates at least 25times the activity of SEQ ID NO: 4.

TABLE 3 SEQ ID ACTIVITY NO RESIDUE DIFFERENCES (RELATIVE TO (NT/AA)(RELATIVE SEQ ID NO: 2) SEQ ID NO: 4) 1/2 — —¹ 3/4 A80T; A94G; S96V;E145L; L153T; Y190P; V196L; I226V; +¹ Y249W; 5/6 A80T; A94G; S96V;E145L; L153T; Y190P; V196L; I226V; +¹ Y249W 7/8 A80T; A94G; S96V; E145L;F147Q; L153T; Y190P; V196L; ++¹ I226V; Y249W  9/10 A80T; A94G; S96V;E145L; L153T; Y190P; V196L; I226V; +¹ 11/12 A80T; A94G; S96V; E145L;D150L; L153T; Y190P; V196M; ++¹ L199M; I226V 13/14 A80T; S96V; I144V;E145L; L153T; Y190P; V196M; L199M; ++¹ I226V; Y249F 15/16 A80T; A94G;S96V; E145L; F147Q; L153T; Y190P; V196M; ++¹ L199M; I226V 17/18 A80T;A94G; V95M; S96V; I144V; E145L; F147Q; L153T; ++¹ Y190P; V196M; I226V;Y249F 19/20 A80T; A94G; V95M; S96V; I144V; E145L; L153T; Y190P; ++¹V196L; L199M; I226V 21/22 L17M; A80T; A94G; S96V; I144V; E145L; F147M;D150L; +++² L153T; Y190P; P194R; V196M; L199M; I226V 23/24 V43R; A64V;T71P; A80T; V87L; A94G; S96V; E145L; F147Q; +++¹ L153T; D173L; Y190P;V196M; L199M; I226V 25/26 V43R; A64V; A80T; A94G; S96V; E145L; F147Q;L153T; +++¹ D173L; Y190P; V196M; L199M; I226V; D233G 27/28 H40R; V43R;A64V; T71P; A80T; V87L; A94G; S96V; E145L; +++² F147Q; L153T; D173L;Y190P; V196M; L199M; I226V; 29/30 E29T; H40R; V43R; A64V; T71P; T76A;A80T; V87L; A94G; +++³ V95Y; S96R; E145L; F147Q; T152L; L153T; N157C;D173L; Y190P; V196M; L199M; E200P; I226V 31/32 E29T; H40R; V43R; A64V;T71P; A80T; V87L; A94G; V95Y; +++³ S96R; N131C; E145L; F147Q; T152A;L153T; D173L; Y190P; V196M; L199M; I226V 33/34 E29T; H40R; A64V; T71P;A80T; V87L; A94G; V95Y; S96R; ++++³ N131C; E145L; F147Q; T152A; L153T;D173L; Y190P; V196M; L199M; E200P; I226V 35/36 L17H; D25T; E29T; H40R;A64V; T71G; A80T; V87L; A94G; ++++³ V95Y; S96R; N131C; E145L; F147Q;T152A; L153T; N157S; D173L; Y190P; V196M; L199M; E200P; I226V 37/38L17H; E29T; H40R; A64V; T71P; A80T; V87L; A94G; V95Y; ++++³ S96R; N131C;E145L; F147Q; T152A; L153T; N157S; D173L; Y190P; V196M; L199M; E200P;I226V ¹Substrate: 5 g/L; DMSO: 5% (v/v); Polypeptide: 10 μL; IPA: 70%(v/v); buffer: 20% (v/v) of 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0);plates heat sealed and shaken (570-575 rpm) overnight at 40° C.²Substrate: 100 g/L; no DMSO added; Polypeptide: 10 μL; IPA: 70% (v/v);buffer: 25% (v/v) of 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0); plates heatsealed and shaken (575 rpm) overnight at 50° C. ³Substrate: 100 g/L; noDMSO added; Polypeptide: 10 μL; IPA: 70% (v/v); buffer: 24% (v/v) of0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0); plates heat sealed and shaken(575 rpm) overnight at 57° C.

Additional information on the functional role of residue positions ofthe Lactobacillus ketoreductase of SEQ ID NO:2 can be found inreferences US 20080318295A1; US 20090093031A1; US 20090155863A1; US20090162909A1; US 20090191605A1; US 20100055751A1; WO/2010/025238A2;WO/2010/025287A2; US 20100062499A1; and WO 2008/151324A1.

Of particular relevance for conversion of compound (2c) or a structuralanalog thereof to compound (1c) or corresponding structural analog areketoreductases with an amino acid sequence comprising one or moreresidue differences as compared to SEQ ID NO:2 at the following residuepositions: X17, X25, X29, X40, X43, X64, X71, X76, X80, X87, X94, X95,X96, X131, X144, X145, X147, X150, X152, X153, X157, X173, X190, X194,X195, X196, X199, X200, X226, X233, and X249. The amino acid differencesat these residue positions are based on locations or regions in thestructure of reference polypeptide (e.g., SEQ ID NO: 2) and/or theassociated functional properties as identified in the exemplaryengineered ketoreductases of Table 3 above.

Further, in some embodiments, the non-naturally occurring engineeredketoreductases, in addition to converting compound (2c) to compound(1c), can also function as a secondary alcohol dehydrogenase of aco-factor recycling system, as described above, and thereby recycle theco-factor NADP+ or NAD+ to NADPH or NADH, respectively, in presence of asecondary alcohol. This property provides increases in efficiency ofconversion of compound (2c) to compound (1c).

Accordingly, in some embodiments, a non-naturally occurring orengineered ketoreductase polypeptide of the present disclosure caninclude an amino acid substitution at a particular residue at a locationin the structure of the reference polypeptide as identified in Table 2,particularly residue positions X17, X25, X29, X40, X43, X64, X71, X76,X80, X87, X94, X95, X96, X131, X144, X145, X147, X150, X152, X153, X157,X173, X190, X194, X195, X196, X199, X200, X226, X233, and X249, withexemplary substitutions at each of the relevant locations identified inTable 3.

Moreover, while the exemplary ketoreductases disclosed herein are basedon the ketoreductase represented by SEQ ID NO:2 from Lactobacilluskefir, it is to be understood that non-naturally occurringketoreductases can be based on the ketoreductase polypeptides from otherLactobacillus species, where the naturally occurring ketoreductase hasat least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, or 99% sequence identity to the polypeptide of SEQ IDNO:2, such as the ketoreductase of Lactobacillus brevis (Genbank Acc.No. 1NXQ_A; GI: 30749782).

In view of the foregoing, in some embodiments, the ketoreductase capableof converting compound (2c) or a structural analog thereof to compound(1c) or corresponding structural analog in enantiomeric excess,comprises an amino acid sequence that has at least 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequenceidentity to a reference polypeptide selected from SEQ ID NO:6, 8, 10,12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, is a non-naturally occurringketoreductase that comprises an amino acid sequence that has at least80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% sequence identity to the reference polypeptide of SEQ ID NO:10.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, is a non-naturally occurringketoreductase that comprises an amino acid sequence that has at least80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% sequence identity to the reference polypeptide of SEQ ID NO:16.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, is a non-naturally occurringketoreductase that comprises an amino acid sequence that has at least80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% sequence identity to a reference polypeptide of SEQ IDNO:36. In some embodiments, the ketoreductase polypeptide comprises anamino acid sequence that has at least 93% sequence identity to SEQ IDNO: 36.

In some embodiments, the ketoreductase useful in the processes hereinand having the specified sequence identity to any of the referencepolypeptides, is capable of converting compound (2c) to compound (1c)with activity equal to or with at least 2-fold, at least 10-fold, atleast 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, orat least 35-fold or more increased activity relative to the activity ofthe polypeptide of SEQ ID NO: 4.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess and having the specifiedsequence identity to any of the reference polypeptides, is capable ofconverting compound (2c) to compound (1c) in at least 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, or 99% enantiomeric excess.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess and having the specifiedsequence identity above to any of the reference polypeptides, has anamino acid sequence that comprises one or more of the followingfeatures: X17 is H or M; X29 is T; X40 is R; X43 is R or V; X64 is V;X71 is P or G; X80 is T; X87 is L; X94 is G; X95 is Y or M; X96 is V orR; X131 is C; X145 is L; X147 is Q or M; X152 is L or A; X153 is T; X173is L; X190 is P; X196 is L or M; X199 is M; X200 is P and X226 is V.

In some embodiments, the present disclosure provides a non-naturallyoccurring polypeptide having ketoreductase activity and the specifiedsequence identity to any of the reference polypeptides disclosed herein,which also has one or more of the following substitutions not previouslyknown in ketoreductase polypeptides derived from naturally occurringLactobacillus ketoreductases: L17H; E29T; V43R; T71P or G; V87L; V95Y;N131C; D173L; or L199M. In particular, it was not known thatnon-naturally occurring polypeptides having ketoreductase activity couldbe derived from naturally occurring Lactobacillus ketoreductases whileincluding substitutions at the following positions: T71 (or X71), V87(X87), or N131 (X131). Accordingly, in some embodiments, the presentdisclosure provides a non-naturally occurring polypeptide havingketoreductase activity which comprises an amino acid sequence that hasat least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, or 99% sequence identity to a reference polypeptideselected from SEQ ID NO:6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28,30, 32, 34, 36, and 38, and which further comprises an amino acidsequence that comprises one or more of the following features: X17 is H;X29 is T; X43 is R; X71 is P or G; X87 is L; X95 is Y; X131 is C; X173is L; and X199 is M. Further, in some embodiments, the non-naturallyoccurring polypeptide having ketoreductase activity comprising one ormore of the following features: X17 is H; X29 is T; X43 is R; X71 is Por G; X87 is L; X95 is Y; X131 is C; X173 is L; and X199 is M, also iscapable of converting compound (2c) or a structural analog thereof tocompound (1c) or corresponding structural analog in enantiomeric excess.

In some embodiments, the present disclosure provides a non-naturallyoccurring polypeptide having ketoreductase activity which comprises anamino acid sequence that has at least 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to areference polypeptide selected from SEQ ID NO:6, 8, 10, 12, 14, 16, 18,20, 22, 24, 26, 28, 30, 32, 34, 36, and 38, and which further comprisesan amino acid sequence that comprises an amino acid difference at one ormore of the following positions: X17, X87, or X131. In some embodiments,the amino acid differences are selected from: X17 is H; X87 is L; orX131 is C. Further, in some embodiments, the non-naturally occurringpolypeptide having ketoreductase activity comprising an amino aciddifference at one or more of the following positions X17, X87, or X131is capable of converting compound (2c) or a structural analog thereof tocompound (1c) or corresponding structural analog in enantiomeric excess.

In some embodiments of the process, the ketoreductase capable ofconverting compound (2c) or a structural analog thereof to compound (1c)or corresponding structural analog in enantiomeric excess and having thespecified sequence identity to any of the reference polypeptides, has anamino acid sequence that comprises one or more of the followingfeatures: X80 is T; X96 is V or R; X145 is L; X153 is T; X190 is P; X196is L or M; and X226 is V.

In some embodiments, the amino acid sequence with one or more of thespecified features at residue positions X80, X96, X145, X153, X190,X196, and X226, further comprises one or more of the following features:X17 is H or M; X29 is T; X40 is R; X43 is R or V; X64 is V; X71 is P orG; X87 is L; X94 is G; X95 is Y or M; X131 is C; X147 is Q or M; X152 isL or A; X173 is L; X199 is M; and X200 is P.

In some embodiments, any of the ketoreductase amino acid sequences abovefurther comprises one or more of the following features: X25 is T; X76is A; X144 is V; X150 is L; X157 is C or S; X194 is R; X233 is G; andX249 is W or F.

In another aspect, in accordance with the above, the present disclosurefurther relates to engineered ketoreductase polypeptides that can beused in the processes described herein and having enzymatic activity inconverting compound (2c) or structural analog thereof to compound (1c)or corresponding structural analog that is equal to or at least 2-fold,at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold,at least 30-fold, or at least 35-fold or more relative to the activityof the polypeptide of SEQ ID NO: 4. In these embodiments, theketoreductase polypeptides are also capable of producing compound (1c)in at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%enantiomeric excess.

Accordingly, in some embodiments, the non-naturally occurringketoreductase polypeptide for use in the processes disclosed herein andcapable of converting compound (2c) or structural analog thereof tocompound (1c) or corresponding structural analog in enantiomeric excesswith activity that is equal to or with at least 2-fold, at least10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least30-fold, or at least 35-fold or more activity of the polypeptide of SEQID NO:4 comprises an amino acid sequence that has at least 80%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%identity to a reference amino acid sequence selected from any one of SEQID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36,or 38, with the proviso that the amino acid sequence comprises any oneof the set of residue differences as compared to SEQ ID NO: 2 containedin any one of the polypeptide sequences of SEQ ID NO:4 to SEQ ID NO:38listed in Table 3.

In some embodiments, the non-naturally occurring ketoreductase capableof converting compound (2c) or structural analog thereof to compound(1c) or corresponding structural analog in enantiomeric excess withactivity that is equal to or with at least 2-fold, at least 10-fold, atleast 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, orat least 35-fold or more activity of the polypeptide of SEQ ID NO:4comprises an amino acid sequence that has at least 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequenceidentity to a reference polypeptide SEQ ID NO: 10, and further comprisesa set of amino acid residue differences as compared to SEQ ID NO:2 ofany one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30,32, 34, 36, and 38.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, is a non-naturally occurringketoreductase that comprises an amino acid sequence that has at least80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% sequence identity to the reference polypeptide SEQ ID NO:16, and further comprises a set of amino acid residue differences ascompared to SEQ ID NO:2 of any one of SEQ ID NO: 6, 8, 10, 12, 14, 16,18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38.

In some embodiments, the ketoreductase capable of converting compound(2c) or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, is a non-naturally occurringketoreductase that comprises an amino acid sequence that has at least80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% sequence identity to a reference polypeptide of SEQ ID NO:36 and further comprises a set of amino acid residue differences ascompared to SEQ ID NO:2 of any one of SEQ ID NO: 6, 8, 10, 12, 14, 16,18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38. In some embodiments, theketoreductase polypeptide comprises an amino acid sequence that has atleast 93% sequence identity to SEQ ID NO: 36, and further comprises aset of amino acid residue differences as compared to SEQ ID NO:2 of anyone of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32,34, 36, and 38.

In some embodiments, in addition to the set of amino acid residuedifferences of any one of the non-naturally occurring polypeptides ofSEQ ID NO: 4 through SEQ ID NO: 38 in the embodiments above, thesequence of the non-naturally occurring polypeptide can further comprise1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-11, 1-12, 1-14, 1-15,1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40 residue differencesat other amino acid residue positions as compared to the SEQ ID NO: 2.In some embodiments, the residue differences can comprise conservativesubstitutions and non-conservative substitutions as compared to SEQ IDNO: 2.

In some embodiments, the ketoreductase capable of converting compound(2c) or structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess and having the specifiedsequence identity to any of the reference polypeptides described herein,has an amino acid sequence that comprises at least the followingfeatures: X80 is T; X96 is V or R; X145 is L; X153 is T; X190 is P; X196is L or M; and X226 is V.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at residue positions X80, X96, X145, X153, X190,X196, and X226, further comprises one or more of the following features:X71 is P or G; X87 is L; and X131 is C.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at residue positions X80, X96, X145, X153, X190,X196, and X226, and X71, X87, and X131 above can further comprise one ormore of the following features: X17 is H or M; X29 is T; X40 is R; X43is R or V; X64 is V; X94 is G; X95 is Y or M; X147 is Q or M; X152 is Lor A; X173 is L; X199 is M; and X200 is P.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at the residue positions indicated above can furthercomprise one or more of the following features: X25 is T; X76 is A; X144is V; X150 is L; X157 is C or S;

X194 is R; X233 is G; and X249 is W or F.

In some embodiments, the ketoreductase capable of converting compound(2c) or structural analog to compound (1c) or corresponding structuralanalog in enantiomeric excess and having the specified sequence identityto any of the reference polypeptides, has an amino acid sequence thatcomprises at least the following features: X64 is V; X71 is P; X80 is T;X87 is L; X94 is A or G; X96 is V; X145 is L; X147 is Q or M; X153 is T;X173 is L; X190 is P; X196 is M; X199 is M; and X226 is V.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at residue positions X64, X71, X80, X87, X94, X96,X145, X147, X153, X173, X190, X196, X199 and X226, further comprises oneor more of the following features: X17 is M or H; X29 is T; X40 is R;X43 is R or V; X95 is M or Y; X131 is C; X152 is L or A; and X200 is P.

In some embodiments, the ketoreductase amino acid sequence with thespecified features at the residue positions indicated above can furthercomprise one or more of the following features: X25 is T; X76 is A; X144is V; X150 is L; X157 is C or S; X194 is R; X233 is G; and X249 is W orF.

In some embodiments, the ketoreductase capable of converting compound(2c) or structural analog to compound (1c) or corresponding structuralanalog in enantiomeric excess and having the specified sequence identityto any of the reference polypeptides, has an amino acid sequence thatcomprises at least the following features: X17 is H or M; X25 is T; X29is T; X40 is R; X43 is R or V; X64 is V; X71 is G or P; X80 is T; X87 isL; X94 is G; X95 is Y or M; X96 is R or V; X131 is C; X145 is L; X147 isQ or M; X152 is A or L; X153 is T; X157 is S or C; X173 is L; X190 is P;X196 is M or L; X199 is M; X200 is P; and X226 is V.

In some embodiments, the ketoreductase with the preceding specifiedfeatures can further comprise one or more of the following features: X76is A; X144 is V; X150 is L; X194 is R; X233 is G; and X249 is W or F.

In some embodiments, the non-naturally occurring ketoreductasepolypeptides capable of converting compound (2c) or structural analogthereof to compound (1c) or corresponding structural analog, comprisesan amino acid sequence selected from SEQ ID NO: 6, 8, 10, 12, 14, 16,18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38.

In a further aspect, engineered ketoreductase polypeptides of moregeneral applicability to conversion of protostereomeric ketones to thecorresponding chiral alcohols can be made in view of thestructure-function information provided herein. In some embodiments, thepolypeptides useful for conversion of a ketone to a correspondingalcohol comprises an amino acid sequence having residue differences ascompared to SEQ ID NO:2 at one or more residue positions selected fromX71, X87 and X131, where the polypeptide has ketoreductase activity. Thestructure-function information indicates that residues X71 and X131occupy the surface of the enzyme while residue X87 is at the interfacebetween the subunits of the tetrameric enzyme. Residues changes ascompared to the wild-type sequence of SEQ ID NO:2 at the specifiedpositions affects solvent stability and/or thermostability, indicatinggeneral application to other engineered ketoreductases.

Accordingly, in some embodiments, an engineered ketoreductasepolypeptide comprises an amino acid sequence that has at least 80%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or99% sequence identity to the reference polypeptide of SEQ ID NO:2 andcomprises at least one or more residue differences as compared to SEQ IDNO:2 at residue positions X71, X87 and X131, wherein the polypeptide hasketoreductase activity.

In some embodiments, an engineered ketoreductase polypeptide comprisesan amino acid sequence that has at least 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity toa reference polypeptide selected from SEQ ID NO:6, 8, 10, 12, 14, 16,18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38 and comprises at leastone or more residue differences as compared to SEQ ID NO:2 at residuepositions X71, X87 and X131, wherein the polypeptide has ketoreductaseactivity.

In some embodiments, the engineered ketoreductase polypeptide comprisesan amino acid sequence having any of the specified percent identitydescribed above and comprising one or more of the following features:X71 is P or G; X87 is L; and X131 is C.

As will be apparent to the skilled artisan, the residues differences atresidue positions X71, X87, and X131 can be combined with other residuechanges that affect various enzyme properties, including among others,enzyme activity, stereoselectivity, thermostability, solvent stability,polypeptide expression, co-factor affinity, or various combinationsthereof. These residue differences include those described in thepresent disclosure (i.e., X17, X25, X29, X40, X43, X64, X71, X76, X80,X87, X94, X95, X96, X131, X144, X145, X147, X150, X152, X153, X157,X173, X190, X194, X195, X196, X199, X200, X226, X233, and X249) andthose described in references disclosing engineered variants of SEQ IDNO:2, including features disclosed in references 20080318295A1; US20090093031A1; US 20090155863A1; US 20090162909A1; US 20090191605A1; US20100055751A1; WO/2010/025238A2; WO/2010/025287A2; and US 20100062499A1,all of which are incorporated herein by reference.

In some embodiments, the polypeptides can comprise deletions of theengineered ketoreductase polypeptides described herein. Thus, for eachand every embodiment of the polypeptides of the disclosure, thedeletions can comprise one or more amino acids, 2 or more amino acids, 3or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 ormore amino acids, 8 or more amino acids, 10 or more amino acids, 15 ormore amino acids, or 20 or more amino acids, up to 10% of the totalnumber of amino acids, up to 10% of the total number of amino acids, upto 20% of the total number of amino acids of the polypeptides, as longas the functional activity of the polypeptide is present, particularlywith respect to the conversion of compound (2c) to compound (1c). Insome embodiments, the deletions can comprise, 1-2, 1-3, 1-4, 1-5, 1-6,1-7, 1-8, 1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22,1-24, 1-26, 1-30, 1-35, or 1-40 amino acid residues. In someembodiments, the number of deletions can be 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, or 40 amino acids.In some embodiments, the deletions can comprise deletions of 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, or 20 amino acidresidues.

In some embodiments, the polypeptides can comprise fragments of theengineered polypeptides described herein. In some embodiments, thefragments can have about 80%, 90%, 95%, 98%, and 99% of the full-lengthpolypeptide, e.g., the polypeptide of SEQ ID NO:4, as long as thefunctional activity of the polypeptide with respect to the conversion ofcompound (2c) to compound (1c) is present.

In some embodiments, the polypeptides of the disclosure can be in theform of fusion polypeptides in which the engineered polypeptides arefused to other polypeptides, such as, by way of example and notlimitation, antibody tags (e.g., myc epitope), purifications sequences(e.g., His tags for binding to metals), and cell localization signals(e.g., secretion signals). Thus, the engineered polypeptides describedherein can be used with or without fusions to other polypeptides.

As will be understood by the skilled artisan, the polypeptides describedherein are not restricted to the genetically encoded amino acids. Inaddition to the genetically encoded amino acids, the polypeptides may becomprised, either in whole or in part, of naturally-occurring and/orsynthetic non-encoded amino acids. Certain commonly encounterednon-encoded amino acids of which the polypeptides described herein maybe comprised include, but are not limited to: the D-enantiomers of thegenetically-encoded amino acids; 2,3-diaminopropionic acid (Dpr);α-aminoisobutyric acid (Aib); ε-aminohexanoic acid (Aha); δ-aminovalericacid (Ava); N-methylglycine or sarcosine (MeGly or Sar); ornithine(Orn); citrulline (Cit); t-butylalanine (Bua); t-butylglycine (Bug);N-methylisoleucine (MeIle); phenylglycine (Phg); cyclohexylalanine(Cha); norleucine (Nle); naphthylalanine (NaI); 2-chlorophenylalanine(Ocf); 3-chlorophenylalanine (Mcf); 4-chlorophenylalanine (Pcf);2-fluorophenylalanine (Off); 3-fluorophenylalanine (Mff);4-fluorophenylalanine (Pff); 2-bromophenylalanine (Obf);3-bromophenylalanine (Mbf); 4-bromophenylalanine (Pbf);2-methylphenylalanine (Omf); 3-methylphenylalanine (Mmf);4-methylphenylalanine (Pmf); 2-nitrophenylalanine (Onf);3-nitrophenylalanine (Mnf); 4-nitrophenylalanine (Pnf);2-cyanophenylalanine (Ocf); 3-cyanophenylalanine (Mcf);4-cyanophenylalanine (Pcf); 2-trifluoromethylphenylalanine (Otf);3-trifluoromethylphenylalanine (Mtf); 4-trifluoromethylphenylalanine(Ptf); 4-aminophenylalanine (Paf); 4-iodophenylalanine (Pif);4-aminomethylphenylalanine (Pamf); 2,4-dichlorophenylalanine (Opef);3,4-dichlorophenylalanine (Mpcf); 2,4-difluorophenylalanine (Opff);3,4-difluorophenylalanine (Mpff); pyrid-2-ylalanine (2pAla);pyrid-3-ylalanine (3pAla); pyrid-4-ylalanine (4pAla); naphth-1-ylalanine(1nAla); naphth-2-ylalanine (2nAla); thiazolylalanine (taAla);benzothienylalanine (bAla); thienylalanine (tAla); furylalanine (fAla);homophenylalanine (hPhe); homotyrosine (hTyr); homotryptophan (hTrp);pentafluorophenylalanine (5ff); styrylkalanine (sAla); authrylalanine(aAla); 3,3-diphenylalanine (Dfa); 3-amino-5-phenypentanoic acid (Afp);penicillamine (Pen); 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid(Tic); β-2-thienylalanine (Thi); methionine sulfoxide (Mso);N(w)-nitroarginine (nArg); homolysine (hLys);phosphonomethylphenylalanine (pmPhe); phosphoserine (pSer);phosphothreonine (pThr); homoaspartic acid (hAsp); homoglutanic acid(hGlu); 1-aminocyclopent-(2 or 3)-ene-4 carboxylic acid; pipecolic acid(PA), azetidine-3-carboxylic acid (ACA);1-aminocyclopentane-3-carboxylic acid; allylglycine (aOly);propargylglycine (pgGly); homoalanine (hAla); norvaline (nVal);homoleucine (hLeu), homovaline (hVal); homoisolencine (hIle);homoarginine (hArg); N-acetyl lysine (AcLys); 2,4-diaminobutyric acid(Dbu); 2,3-diaminobutyric acid (Dab); N-methylvaline (MeVal);homocysteine (hCys); homoserine (hSer); hydroxyproline (Hyp) andhomoproline (hPro). Additional non-encoded amino acids of which thepolypeptides described herein may be comprised will be apparent to thoseof skill in the art (see, e.g., the various amino acids provided inFasman, 1989, CRC Practical Handbook of Biochemistry and MolecularBiology, CRC Press, Boca Raton, Fla., at pp. 3-70 and the referencescited therein, all of which are incorporated by reference). These aminoacids may be in either the L- or D-configuration.

Those of skill in the art will recognize that amino acids or residuesbearing side chain protecting groups may also comprise the polypeptidesdescribed herein. Non-limiting examples of such protected amino acids,which in this case belong to the aromatic category, include (protectinggroups listed in parentheses), but are not limited to: Arg(tos),Cys(methylbenzyl), Cys (nitropyridinesulfenyl), Glu(δ-benzylester),Gln(xanthyl), Asn(N-δ-xanthyl), His(bom), His(benzyl), His(tos),Lys(fmoc), Lys(tos), Ser(O-benzyl), Thr (O-benzyl) and Tyr(O-benzyl).

Non-encoding amino acids that are conformationally constrained of whichthe polypeptides described herein may be composed include, but are notlimited to, N-methyl amino acids (L-configuration); 1-aminocyclopent-(2or 3)-ene-4-carboxylic acid; pipecolic acid; azetidine-3-carboxylicacid; homoproline (hPro); and 1-aminocyclopentane-3-carboxylic acid.

In some embodiments, the engineered ketoreductase polypeptides can beprovided on a solid support, such as a membrane, resin, solid carrier,or other solid phase material. A solid support can be composed oforganic polymers such as polystyrene, polyethylene, polypropylene,polyfluoroethylene, polyethyleneoxy, and polyacrylamide, as well asco-polymers and grafts thereof. A solid support can also be inorganic,such as glass, silica, controlled pore glass (CPG), reverse phase silicaor metal, such as gold or platinum. The configuration of a solid supportcan be in the form of beads, spheres, particles, granules, a gel, amembrane or a surface. Surfaces can be planar, substantially planar, ornon-planar. Solid supports can be porous or non-porous, and can haveswelling or non-swelling characteristics. A solid support can beconfigured in the form of a well, depression, or other container,vessel, feature, or location.

In some embodiments, the engineered polypeptides having ketoreductaseactivity of the present disclosure can be immobilized on a solid supportsuch that they retain their improved activity, stereoselectivity, and/orother improved properties relative to the reference polypeptide of SEQID NO: 4. In such embodiments, the immobilized polypeptides canfacilitate the biocatalytic conversion of the substrate of compound (2c)or structural analogs thereof to the product of compound (1c) orcorresponding structural analogs (e.g., as shown in the process ofScheme 1 described herein), and after the reaction is complete areeasily retained (e.g., by retaining beads on which polypeptide isimmobilized) and then reused or recycled in subsequent reactions. Suchimmobilized enzyme processes allow for further efficiency and costreduction. Accordingly, it is further contemplated that any of themethods of using the engineered ketoreductase polypeptides of thepresent disclosure can be carried out using the same engineeredketoreductase polypeptides bound or immobilized on a solid support.

Methods of enzyme immobilization are well-known in the art. Theengineered ketoreductase polypeptide can be bound non-covalently orcovalently. Various methods for conjugation and immobilization ofenzymes to solid supports (e.g., resins, membranes, beads, glass, etc.)are well known in the art and described in e.g.: Yi et al., “Covalentimmobilization of ω-transaminase from Vibrio fluvialis JS17 on chitosanbeads,” Process Biochemistry 42(5): 895-898 (May 2007); Martin et al.,“Characterization of free and immobilized (S)-aminotransferase foracetophenone production,” Applied Microbiology and Biotechnology 76(4):843-851 (September 2007); Koszelewski et al., “Immobilization ofω-transaminases by encapsulation in a sol-gel/celite matrix,” Journal ofMolecular Catalysis B: Enzymatic, 63: 39-44 (April 2010); Truppo et al.,“Development of an Improved Immobilized CAL-B for the EnzymaticResolution of a Key Intermediate to Odanacatib,” Organic ProcessResearch & Development, published online: dx.doi.org/10.1021/op200157c;Hermanson, G. T., Bioconjugate Techniques, Second Edition, AcademicPress (2008); Mateo et al., “Epoxy sepabeads: a novel epoxy support forstabilization of industrial enzymes via very intense multipoint covalentattachment,” Biotechnology Progress 18(3): 629-34 (2002); andBioconjugation Protocols: Strategies and Methods, In Methods inMolecular Biology, C. M. Niemeyer ed., Humana Press (2004); thedisclosures of each which are incorporated by reference herein. Solidsupports useful for immobilizing the engineered ketoreductases of thepresent disclosure include but are not limited to beads or resinscomprising polymethacrylate with epoxide functional groups,polymethacrylate with amino epoxide functional groups, styrene/DVBcopolymer or polymethacrylate with octadecyl functional groups.Exemplary solid supports useful for immobilizing the engineeredketoreductases of the present disclosure include, but are not limitedto, chitosan beads, Eupergit C, and SEPABEADs (Mitsubishi), includingthe following different types of SEPABEAD: EC-EP, EC-HFA/S, EXA252,EXE119 and EXE120.

In some embodiments, the engineered ketoreductase polypeptides can be invarious forms, for example, such as an isolated preparation, as asubstantially purified enzyme, whole cells transformed with gene(s)encoding the enzyme, and/or as cell extracts and/or lysates of suchcells. The enzymes can be lyophilized, spray-dried, precipitated or bein the form of a crude paste, as further discussed below.

In some embodiments, the polypeptide described herein can be provided inthe form of kits. The enzymes in the kits may be present individually oras a plurality of enzymes. The kits can further include reagents forcarrying out the enzymatic reactions, substrates for assessing theactivity of enzymes, as well as reagents for detecting the products. Thekits can also include reagent dispensers and instructions for use of thekits.

In some embodiments, the polypeptides can be provided on a substrate. Insome embodiments, the polypeptides can be provided in the form of anarray in which the polypeptides are arranged in positionally distinctlocations. The array can be used to test a variety of aryl alkylsulfides for conversion by the polypeptides. “Substrate,” “support,”“solid support,” “solid carrier,” or “resin” in the context of arraysrefer to any solid phase material. Substrate also encompasses terms suchas “solid phase,” “surface,” and/or “membrane.” A solid support can becomposed of organic polymers such as polystyrene, polyethylene,polypropylene, polyfluoroethylene, polyethyleneoxy, and polyacrylamide,as well as co-polymers and grafts thereof. A solid support can also beinorganic, such as glass, silica, controlled pore glass (CPG), reversephase silica or metal, such as gold or platinum. The configuration of asubstrate can be in the form of beads, spheres, particles, granules, agel, a membrane or a surface. Surfaces can be planar, substantiallyplanar, or non-planar. Solid supports can be porous or non-porous, andcan have swelling or non-swelling characteristics. A solid support canbe configured in the form of a well, depression, or other container,vessel, feature, or location. A plurality of supports can be configuredon an array at various locations, addressable for robotic delivery ofreagents, or by detection methods and/or instruments.

In some embodiments, the kits of the present disclosure include arrayscomprising a plurality of different engineered ketoreductasepolypeptides at different addressable position, wherein the differentpolypeptides are different variants of a reference sequence each havingat least one different improved enzyme property. Such arrays comprisinga plurality of engineered polypeptides and methods of their use aredescribed in, e.g., WO2009/008908A2.

5.3 KETOREDUCTASE ENCODING POLYNUCLEOTIDES, EXPRESSION VECTORS AND HOSTCELLS

In another aspect, the present disclosure provides polynucleotidesencoding the non-naturally occurring polypeptides described herein.These polynucleotides may be operatively linked to one or moreheterologous regulatory sequences that control gene expression to createa recombinant polynucleotide capable of expressing the ketoreductasepolypeptide. Expression constructs containing a heterologouspolynucleotide encoding the engineered ketoreductase polypeptide can beintroduced into appropriate host cells to express the correspondingpolypeptide.

Because of the knowledge of the codons corresponding to the variousamino acids, availability of a protein sequence provides a descriptionof all the polynucleotides capable of encoding the subject. Thus, havingidentified a particular amino acid sequence, those skilled in the artcould make any number of different nucleic acids by simply modifying thesequence of one or more codons in a way which does not change the aminoacid sequence of the protein. In this regard, the present disclosurespecifically contemplates each and every possible variation ofpolynucleotides that could be made by selecting combinations based onthe possible codon choices, and all such variations are to be consideredspecifically disclosed for any polypeptide described herein, includingthe amino acid sequences presented in Table 3.

In some embodiments, the polynucleotides can be selected and/orengineered to comprise codons that are preferably selected to fit thehost cell in which the protein is being produced. For example, preferredcodons used in bacteria are used to express the gene in bacteria;preferred codons used in yeast are used for expression in yeast; andpreferred codons used in mammals are used for expression in mammaliancells. Since not all codons need to be replaced to optimize the codonusage of the ketoreductases (e.g., because the natural sequence can havepreferred codons and because use of preferred codons may not be requiredfor all amino acid residues), codon optimized polynucleotides encodingthe ketoreductase polypeptides may contain preferred codons at about40%, 50%, 60%, 70%, 80%, or greater than 90% of codon positions of thefull length coding region.

In some embodiments, the polynucleotide encodes a non-naturallyoccurring polypeptide capable of converting compound (2c) or astructural analog thereof to compound (1c) or corresponding structuralanalog in enantiomeric excess, where the polypeptide comprises an aminoacid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a referencepolypeptide selected from any one of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16,18, 20, 22, 24, 26, 28, 30, 32, 34, 36, and 38.

In some embodiments, the polynucleotide encodes a non-naturallyoccurring ketoreductase polypeptide capable of converting compound (2c)or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, wherein the ketoreductasepolypeptide comprises an amino acid sequence that has at least 80%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%sequence identity to a reference polypeptide SEQ ID NO: 10.

In some embodiments, the polynucleotide encodes a non-naturallyoccurring ketoreductase polypeptide capable of converting compound (2c)or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, wherein the ketoreductasepolypeptide comprises an amino acid sequence that has at least 80%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%sequence identity to the reference polypeptide of SEQ ID NO: 16.

In some embodiments, the polynucleotide encodes a non-naturallyoccurring ketoreductase polypeptide capable of converting compound (2c)or a structural analog thereof to compound (1c) or correspondingstructural analog in enantiomeric excess, wherein the ketoreductasepolypeptide comprises an amino acid sequence that has at least 80%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%sequence identity to a reference polypeptide of SEQ ID NO: 36. In someembodiments, the polynucleotide encodes a ketoreductase polypeptidecomprising an amino acid sequence that has at least 93% sequenceidentity to SEQ ID NO: 36.

In some embodiments, the polynucleotide encodes a non-naturallyoccurring polypeptide capable of converting compound (2c) to compound(1c) with activity equal to or at least 2-fold, at least 10-fold, atleast 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, orat least 35-fold increased relative to the activity of the polypeptideof SEQ ID NO: 4, wherein the polypeptide comprises an amino acidsequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference polypeptideselected from any one of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22,24, 26, 28, 30, 32, 34, 36, or 38, with the proviso that the amino acidsequence comprises any one of the set of residue differences as comparedto SEQ ID NO: 2 contained in any one of the polypeptide sequences of SEQID NO: 4 to SEQ ID NO: 38 listed in Table 3. As discussed herein, insome embodiments, the reference polypeptide is SEQ ID NO: 10, 16 or 36.

In some embodiments, the polynucleotide encodes a non-naturallyoccurring, engineered ketoreductase polypeptide capable of convertingcompound (2c) or a structural analog thereof to compound (1c) orcorresponding structural analog in enantiomeric excess, and having anyof the specified sequence identity to any of the reference polypeptidesdescribed herein, and comprises one or more residue differences ascompared to SEQ ID NO:2 at the following residue positions: X17, X25,X29, X40, X43, X64, X71, X76, X80, X87, X94, X95, X96, X131, X144, X145,X147, X150, X152, X153, X157, X173, X190, X194, X195, X196, X199, X200,X226, X233, and X249. As such, in some embodiments, the polynucleotidesencode the ketoreductase polypeptides having any of the specifiedsequence identity to the reference polypeptides described above andcomprising the specified features at the foregoing residue positions,including sets of residue positions, as provided in the presentdisclosure.

In some embodiments, the polynucleotides encoding the polypeptides areselected from SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27,29, 31, 33, 35, and 37.

In some embodiments, the polynucleotides are capable of hybridizingunder highly stringent conditions to a polynucleotide comprising SEQ IDNO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, or37, or a complement thereof, where the highly stringently hybridizingpolynucleotides encode a non-naturally occurring polypeptide capable ofconverting compound (2c) to compound (1c) with activity equal to or withat least 2-fold, at least 10-fold, at least 15-fold, at least 20-fold,at least 25-fold, at least 30-fold, or at least 35-fold increasedactivity relative to the activity of the polypeptide of SEQ ID NO: 4.

In some embodiments, the polynucleotides encode the polypeptidesdescribed herein but have about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity atthe nucleotide level to a reference polynucleotide encoding theengineered ketoreductase polypeptides described herein. In someembodiments, the reference polynucleotide is selected from SEQ ID NO: 3,5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, and 37.

An isolated polynucleotide encoding a non-naturally occurringpolypeptide of the present disclosure may be manipulated in a variety ofways to provide for expression of the polypeptide. In some embodiments,the polynucleotides encoding the polypeptides can be provided asexpression vectors where one or more control sequences is present toregulate the expression of the polynucleotides and/or polypeptides.Manipulation of the isolated polynucleotide prior to its insertion intoa vector may be desirable or necessary depending on the expressionvector. The techniques for modifying polynucleotides and nucleic acidsequences utilizing recombinant DNA methods are well known in the art.Guidance is provided in Sambrook et al., 2001, Molecular Cloning: ALaboratory Manual, 3rd Ed., Cold Spring Harbor Laboratory Press; andCurrent Protocols in Molecular Biology, Ausubel. F. ed., Greene Pub.Associates, 1998, updates to 2006.

In some embodiments, the control sequences include among others,promoters, leader sequence, polyadenylation sequence, propeptidesequence, signal peptide sequence, and transcription terminator.Suitable promoters can be selected based on the host cells used.Exemplary bacterial promoters include E. coli lac operon, E. coli trpoperon, bacteriophage, Streptomyces coelicolor agarase gene (dagA),Bacillus subtilis levansucrase gene (sacB), Bacillus licheniformisalpha-amylase gene (amyL), beta-lactamase gene, and tac promoter;exemplary promoters for filamentous fungal host cells, include promotersobtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucormiehei aspartic proteinase, Aspergillus niger neutral alpha-amylase,Aspergillus niger acid stable alpha-amylase, Aspergillus niger orAspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase,Aspergillus oryzae alkaline protease, Aspergillus oryzae triosephosphate isomerase, Aspergillus nidulans acetamidase, and Fusariumoxysporum trypsin-like protease, and mutant, truncated, and hybridpromoters thereof, and exemplary yeast cell promoters can be from thegenes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomycescerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), andSaccharomyces cerevisiae 3-phosphoglycerate kinase.

In some embodiments, the control sequence may also be a signal peptidecoding region that codes for an amino acid sequence linked to the aminoterminus of a polypeptide and directs the encoded polypeptide into thecell's secretory pathway. The signal sequence typically depends on thetype of host cells being used to express the polypeptide. Effectivesignal peptide coding regions for bacterial host cells are the signalpeptide coding regions obtained from the genes for Bacillus NClB 11837maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacilluslicheniformis subtilisin, Bacillus licheniformis beta-lactamase,Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), andBacillus subtilis prsA. Exemplary signal peptide coding regions forfilamentous fungal host cells can be the signal peptide coding regionsobtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillusniger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor mieheiaspartic proteinase, Humicola insolens cellulase, and Humicolalanuginosa lipase. Useful signal peptides for yeast host cells can befrom the genes for Saccharomyces cerevisiae alpha-factor andSaccharomyces cerevisiae invertase.

Other control sequences, such as leader sequences, polyadenylationsequences, and transcription terminator sequences can use thoseavailable in the art (see Sambrook, supra, and Current Protocols inMolecular Biology, supra).

In another aspect, the present disclosure is also directed to arecombinant expression vector comprising a polynucleotide encoding anengineered ketoreductase polypeptide, and one or more expressionregulating regions such as a promoter and a terminator, a replicationorigin, etc., depending on the type of hosts into which they are to beintroduced. The recombinant expression vector may be any vector (e.g., aplasmid or virus), which can be conveniently subjected to recombinantDNA procedures and can bring about the expression of the polynucleotidesequence. The choice of the vector will typically depend on thecompatibility of the vector with the host cell into which the vector isto be introduced. The vectors may be linear or closed circular plasmids.

The expression vector may be an autonomously replicating vector, i.e., avector that exists as an extrachromosomal entity, the replication ofwhich is independent of chromosomal replication, e.g., a plasmid, anextrachromosomal element, a minichromosome, or an artificial chromosome.The vector may contain any means for assuring self-replication.Alternatively, the vector may be one which, when introduced into thehost cell, is integrated into the genome and replicated together withthe chromosome(s) into which it has been integrated. The expressionvector preferably contains one or more selectable markers, which permiteasy selection of transformed cells. A selectable marker is a gene theproduct of which provides for biocide or viral resistance, resistance toheavy metals, prototrophy to auxotrophs, resistance to chemical agents(e.g., antibiotics) and the like.

In another aspect, the present disclosure provides a host cellcomprising a polynucleotide encoding an engineered ketoreductasepolypeptide of the present disclosure, the polynucleotide beingoperatively linked to one or more control sequences for expression ofthe ketoreductase polypeptide in the host cell. Host cells for use inexpressing the ketoreductase polypeptides encoded by the expressionvectors of the present invention are well known in the art and includebut are not limited to, bacterial cells, such as E. coli, Lactobacillus,Streptomyces and Salmonella typhimurium cells; fungal cells, such asyeast cells; insect cells such as Drosophila S2 and Spodoptera Sf9cells; animal cells such as CHO, COS, BHK, 293, and Bowes melanomacells; and plant cells. Exemplary host cells are Escherichia coli BL21and W3110.

Appropriate culture mediums and growth conditions for theabove-described host cells are well known in the art. Polynucleotidesfor expression of the ketoreductase may be introduced into host cells byvarious methods known in the art (e.g., electroporation, biolisticparticle bombardment, liposome mediated transfection, calcium chloridetransfection, and protoplast fusion).

In the embodiments herein, the non-naturally occurring or engineeredketoreductase polypeptides and nucleotides encoding such polypeptidescan be prepared using methods commonly used by those skilled in the art.As noted above, the naturally-occurring amino acid sequence andcorresponding polynucleotide encoding the ketoreductase enzyme ofLactobacillus kefir for use in generating engineered ketoreductases areavailable as Genbank Acc. No. AAP94029.1; GI: 33112056. In someembodiments, the parent polynucleotide sequence is codon optimized toenhance expression of the ketoreductase in a specified host cell.

The engineered ketoreductase polypeptides can be obtained by subjectingthe polynucleotide encoding the naturally occurring ketoreductase tomutagenesis and/or directed evolution methods (see, e.g., Stemmer, 1994,Proc Natl Acad Sci USA 91:10747-10751; PCT Publ. Nos. WO 95/22625, WO97/0078, WO 97/35966, WO 98/27230, WO 00/42651, and WO 01/75767; U.S.Pat. Nos. 6,537,746; 6,117,679; 6,376,246; and 6,586,182; and U.S. Pat.Publ. Nos. 20080220990A1 and 20090312196A1; each of which is herebyincorporated by reference herein).

Other directed evolution procedures that can be used include, amongothers, staggered extension process (StEP), in vitro recombination (Zhaoet al., 1998, Nat. Biotechnol. 16:258-261), mutagenic PCR (Caldwell etal., 1994, PCR Methods Appl. 3:S136-S140), and cassette mutagenesis(Black et al., 1996, Proc Natl Acad Sci USA 93:3525-3529). Mutagenesisand directed evolution techniques useful for the purposes herein arealso described in the following references: Ling, et al., 1997, Anal.Biochem. 254(2):157-78; Dale et al., 1996, Methods Mol. Biol. 57:369-74;Smith, 1985, Ann. Rev. Genet. 19:423-462; Botstein et al., 1985, Science229:1193-1201; Carter, 1986, “Site-directed mutagenesis,” Biochem. J.237:1-7; Kramer et al., 1984, Cell 38:879-887; Wells et al., 1985, Gene34:315-323; Minshull et al., 1999, Curr Opin Chem Biol 3:284-290;Christians et al., 1999, Nature Biotech 17:259-264; Crameri et al.,1998, Nature 391:288-291; Crameri et al., 1997, Nature Biotech15:436-438; Zhang et al., 1997, Proc Natl Acad Sci USA 94:45-4-4509;Crameri et al., 1996, Nature Biotech 14:315-319; and Stemmer, 1994,Nature 370:389-391. All publications are incorporated herein byreference.

In some embodiments, the clones obtained following mutagenesis treatmentare screened for non-naturally occurring ketoreductases having a desiredenzyme property. Measuring ketoreductase enzyme activity from theexpression libraries can be performed using standard techniques, such asseparation of the product (e.g., by HPLC or GC) and detection of theproduct by measuring UV absorbance of the separated substrate andproducts and/or by detection using tandem mass spectroscopy (e.g.,MS/MS). Clones containing a polynucleotide encoding the desiredengineered polypeptides are then isolated, sequenced to identify thenucleotide sequence changes (if any), and used to express the enzyme ina host cell. Exemplary assays are provided below in Example 3.

Where the sequence of the polypeptide is known, the polynucleotidesencoding the enzyme can be prepared by standard solid-phase methods,according to known synthetic methods, e.g., the classicalphosphoramidite method described by Beaucage et al., 1981, Tet Lett22:1859-69, or the method described by Matthes et al., 1984, EMBO J.3:801-05. In some embodiments, fragments of up to about 100 bases can beindividually synthesized, then joined (e.g., by enzymatic or chemicallitigation methods, or polymerase mediated methods) to form any desiredcontinuous sequence.

In some embodiments, the present disclosure also provides methods forpreparing or manufacturing the non-naturally occurring polypeptidescapable of converting compound (2c) to compound (1c), wherein themethods comprise culturing a host cell capable of expressing apolynucleotide encoding the non-naturally occurring polypeptide underconditions suitable for expression of the polypeptide. In someembodiments, the method for preparing or manufacturing the non-naturallyoccurring ketoreductase polypeptide further comprises the step ofisolating the polypeptide from the host cell. The non-naturallyoccurring polypeptides can be expressed in appropriate cells, asdescribed above, and isolated (or recovered) from the host cells and/orthe culture medium using any one or more of the well known techniquesused for protein purification, including, among others, lysozymetreatment, sonication, filtration, salting-out, ultra-centrifugation,and chromatography. Chromatographic techniques for isolation of theketoreductase polypeptide include, among others, reverse phasechromatography high performance liquid chromatography, ion exchangechromatography, gel electrophoresis, and affinity chromatography.

In some embodiments, the non-naturally occurring polypeptide of thedisclosure can be prepared and used in various isolated forms includingbut not limited to crude extracts (e.g., cell-free lysates), powders(e.g., shake-flask powders), lyophilizates, and substantially purepreparations (e.g., DSP powders), as further illustrated in the Examplesbelow.

In some embodiments, the non-naturally occurring polypeptide of thedisclosure can be prepared and used in purified form. Generally,conditions for purifying a particular enzyme will depend, in part, onfactors such as net charge, hydrophobicity, hydrophilicity, molecularweight, molecular shape, etc., and will be apparent to those havingskill in the art. To facilitate purification, it is contemplated that insome embodiments the engineered ketoreductase polypeptides of thepresent disclosure can be expressed as fusion proteins with purificationtags, such as His-tags having affinity for metals, or antibody tags forbinding to antibodies, e.g., myc epitope tag.

6. EXAMPLES

Various features and embodiments of the disclosure are illustrated inthe following representative examples, which are intended to beillustrative, and not limiting.

Example 1 Wild-Type Ketoreductase Gene Acquisition and Construction ofExpression Vectors

The wild-type ketoreductase gene from L. kefir (SEQ ID NO: 1) wasdesigned for expression in E. coli using standard codon optimization.(Codon-optimization software is reviewed in e.g., “OPTIMIZER: a webserver for optimizing the codon usage of DNA sequences,” Puigbò et al.,Nucleic Acids Res. 2007 July; 35(Web Server issue): W126-31. Epub 2007Apr. 16.) Genes were synthesized using oligonucleotides composed of 42nucleotides and cloned into expression vector pCK110900 (vector depictedas FIG. 3 in US Patent Application Publication 20060195947, which ishereby incorporated by reference herein) under the control of a lacpromoter. The expression vector also contained the P15a origin ofreplication and the chloramphenicol resistance gene. Resulting plasmidswere transformed into E. coli W3110 (fhu-) using standard methods.Polynucleotides encoding the engineered ketoreductase polypeptides werealso cloned into vector pCK110900 for expression in E. coli W3110.

The engineered ketoreductase polypeptide of SEQ ID NO: 4 was obtained bydirected evolution of a codon-optimized gene encoding the wild-typeketoreductase of Lactobacillus kefir (Genbank acc. No. AAP94029.1; GI:33112056). SEQ ID NO: 4 has 9 amino acid residue differences relative tothe WT ketoreductase (A80T, A94G, S96V, E145L, L153T, Y190P, V196L,1226V, and Y249W) of SEQ ID NO:2. The polypeptide of SEQ ID NO: 4 wasfound to be able to convert compound (2c) to compound (1c) in >99% e.e.and with about 25% conversion rate in 24 h under initial screeningconditions (100 g/L compound (2a) substrate; 0.5 g/L NADP, 100 mM TEA,pH 9.0, 1 mM MgSO₄, 40° C.). The polypeptide SEQ ID NO: 4 was used asthe starting backbone for subsequent rounds of evolution. Multiplerounds of directed evolution of the gene encoding SEQ ID NO: 4 (i.e.,SEQ ID NO: 3) were carried out. Each round used the gene encoding themost improved engineered polypeptide from each round as the parent“backbone” sequence for the subsequent round of evolution. The resultingengineered ketoreductase polypeptide sequences and specific mutationsand relative activities are listed in Table 3.

Example 2 Production of Engineered Polypeptides

The engineered ketoreductase polypeptides of the disclosure wereproduced in E. coli W3110 as an intracellular protein expressed underthe control of the lac promoter. The polypeptide accumulates primarilyas a soluble cytosolic active enzyme. A shake-flask procedure is used togenerate engineered polypeptide powders that can be used in activityassays or biocatalytic process disclosed herein.

Fermentation for Shake Flask Powders.

A single microbial colony of E. coli containing a plasmid encoding anengineered ketoreductase of interest is inoculated into 50 mL LuriaBertani broth containing 30 μg/mlchloramphenicol and 1% glucose. Cellsare grown overnight (at least 16 hours) in an incubator at 30° C. withshaking at 250 rpm. The culture is diluted into 250 mL Terrific Broth(12 g/L bacto-tryptone, 24 g/L yeast extract, 4 mL/L glycerol, 65 mMpotassium phosphate, pH 7.0, 1 mM MgSO₄) containing 30 μg/mlchloramphenicol, in a 1 liter flask to an optical density at 600 nm(OD₆₀₀) of 0.2 and allowed to grow at 30° C. Expression of theketoreductase gene is induced by addition ofisopropyl-β-D-thiogalactoside (“IPTG”) to a final concentration of 1 mMwhen the OD600 of the culture is 0.6 to 0.8. Incubation is thencontinued overnight (at least 16 hours). Cells are harvested bycentrifugation (5000 rpm, 15 min, 4° C.) and the supernatant discarded.

Production of Ketoreductase Shake-Flask Powders:

The cell pellet is resuspended with an equal volume of cold (4° C.) 100mM phosphate buffer, pH 9.0 (optionally including 2 mM MgSO₄), andharvested by centrifugation as above. The washed cells are resuspendedin two volumes of the cold phosphate buffer and passed through a FrenchPress twice at 12,000 psi while maintained at 4° C. Cell debris isremoved by centrifugation (9000 rpm, 45 minutes, 4° C.). The clearlysate supernatant was collected and stored at −20° C. Lyophilization offrozen clear lysate provides a dry shake-flask powder of crudeketoreductase polypeptide. Alternatively, the cell pellet (before orafter washing) can be stored at 4° C. or −80° C.

Fermentation for Production Downstream Process (DSP) Powders.

Larger-scale (˜100-120 g) fermentation of the engineered ketoreductasesfor production of DSP powders can be carried out as a short batchfollowed by a fed batch process according to standard bioprocessmethods. Briefly, ketoreductase expression is induced by addition ofIPTG to a final concentration of 1 mM. Following fermentation, the cellsare harvested and resuspended in 100 mM triethanolamine-H₂SO₄ buffer,then mechanically disrupted by homogenization. The cell debris andnucleic acid are flocculated with polyethylenimine (PEI) and thesuspension clarified by centrifugation. The resulting clear supernatantis concentrated using a tangential cross-flow ultrafiltration membraneto remove salts and water. The concentrated and partially purifiedenzyme concentrate can then be dried in a lyophilizer and packaged(e.g., in polyethylene containers).

Example 3 High Throughput (HTP) Assay Protocols

High-Throughput Growth & Expression.

Cells were picked and grown using standard KRED protocol for W3110 withdirect induction: (1) Master growth=single colonies picked from agarQ-trays by Q-bot and grown overnight in LB media containing 1% glucoseand 30 μg/mL chloramphenicol (CAM), 30° C., 200 rpm, 85% humidity. (2)Subculture=20 μL of overnight growth transferred to a deep well platecontaining 380 μL 2×YT growth media containing 30 μg/mL CAM, 1 mM IPTG,1 mM MgSO₄, and incubated for ˜18 h at 30° C., 200 rpm, 85% humidity.Subculture TB media was made up of TB media (380 μL/well), 30 μg/mL CAM,1 mM MgSO₄, and 1 mM IPTG. Cell culture was centrifuged at 4000 rpm, 4°C. for 10 min, and the media discarded. Cell pellets were resuspended in200-400 μL lysis buffer (0.1 M triethanolamine (TEA) buffer, pH 9.0,containing 1 mM MgSO₄, 400 μg/mL PMBS and 500 μg/mL Lysozyme).

HTP Screening Procedure.

Standard HTP reaction assays were carried out on 200 μL reaction volumescales in 96-wells deep well plates (reaction assay blocks). Thereaction mixtures in each well typically consisted of: 5.0 g/L substrateoxcarbazepine prepared in DMSO or approximately 80 g/L solid substrateoxcarbazepine; 0.05 g/L NADP⁺; 70% isopropyl alcohol (IPA); 0, 0.5 or 1%acetone; and 10 μL, 20 μL or 50 μL of clear lysates, as furtherspecified below. Generally, reaction reagents were added using automatedHTP robotics, such as Biomek NX. Lysis volumes were fixed at 150 μL or300 μL. In later rounds, lysates were diluted 2× or 0.6× after lysis.

Assay Protocols I and II.

Cell lysates were prepared by one of two methods. Cell pellets werelysed with 300 μL/well lysis buffer (1.0 mg/mL lysozyme, 0.5 mg/mL PMBSin 0.1M TEA-HCl with 1 mM MgSO₄, pH 9.0) for plates grown using TBmedium as subculture media. 150 μL/well or 300 μL/well lysis buffer wasused for plates grown using 2×YT medium as subculture media. Lysateswere also prepared by lysing cell pellets with 300 μL/well lysis bufferfor plates grown using TB medium as subculture media and then 2× dilutedwith 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0) buffer.

Plates were then left to shake at speed of 1.5-2.5 g on a titre-plateshaker, room temperature, for 1.5 hrs. Plates containing lysed cellswere centrifuged at 4000 rpm for 10 min at 4° C. Plates with lysateswere stored at 4° C. if they were not immediately used.

The reaction condition comprised oxcarbazepine, 5 g/L (5% v/v DMSO);NADP⁺, 0.05 g/L; IPA 70% v/v; and lysate, 10 μL or 20 μL. Assay wascarried out by adding into reaction assay blocks 10 μL/well of 100 g/Lwarmed substrate in DMSO (freshly prepared), 140 μL/well of isopropylalcohol (IPA), and 40 μL/well of 0.25 g/L NADP⁺, prepared in 0.1MTEA-HCl with 1 mM MgSO₄ (pH 9.0). Clear lysates (10 μL/well) from lysateplates were transferred to their reaction mixtures. Plates were heatsealed and left to shake overnight at 40° C. and 570-575 rpm.

For reactions in which cells were lysed in 150 μL/well lysis buffer, 10μL/well of 100 g/L warmed substrate in DMSO, freshly prepared, wereadded into reaction assay blocks. This was followed by the addition of30 μL/well of 0.33 g/L NADP+ prepared in 0.1M TEA-HCl with 1 mM MgSO₄(pH 9.0) followed by 140 μL/well of isopropyl alcohol (IPA). Clearlysates (20 μL/well) from lysate plates were respectively transferred totheir reaction mixtures. Plates were heat sealed and left to shakeovernight at 40° C. and 570 rpm.

Assay Protocol III.

Lysates were prepared as described for Assay Protocols I and II above.The reaction conditions comprised oxcarbazepine, 75 g/L; NADP⁺, 0.05g/L; IPA, 70% v/v; and lysate, 10 μL, 20 μL or 50 μL. Assays werecarried out by dispensing 15 mg substrate solid into reaction assayblocks using solid dose template plate Millipore MACL09625. This wasfollowed by 10 μL/well of 1 g/L NADP⁺ prepared in 0.1M TEA-HCl with 1 mMMgSO₄ (pH 9.0). IPA of 140 μL/well of was then dispensed into the assayblocks. Clear lysates of 50 μL/well from lysate plates were respectivelytransferred to their reaction mixtures. Plates were heat sealed and leftto shake overnight at 45° C. and 575 rpm.

Assay Protocol IV.

Cell pellets were lysed with 300 μL/well lysis buffer and then diluted0.6× with 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0) buffer, and worked up asdescribed in Reactions I and II above. The reaction conditions comprisedoxcarbazepine, 75 g/L; NADP 0.05 g/L; IPA, 70% v/v; and lysate, 10 μL,20 μL or 50 μL. Assays were carried out by dispensing 15-20 mg substratesolid into reaction assay blocks using solid dose template plateMillipore MACL09625. IPA was dispensed into the reaction assay blocks at140 μL/well, followed by 50 μL/well of NADP⁺ 0.2 g/L prepared in 0.1MTEA-HCl with 1 mM MgSO₄ (pH 9.0). Clear lysates of 10 μL/well fromlysate plates were respectively transferred to their reaction mixtures.Plates were heat sealed and left to shake overnight at 50° C. and 575rpm.

Assay Protocol V.

Cell pellets were processed as described in Assay Protocol_IV. Thereaction condition comprised oxcarbazepine, 75 g/L; NADP⁺ 0.05 g/L;IPA/Acetone, 70:0.5% v/v; and lysate 10 μL. Assays were carried out bydispensing 15-20 mg solid substrate into reaction assay blocks usingsolid dose template plate Millipore MACL09625, followed by 49 μL/well of0.2 g/L NADP+ prepared in 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0).IPA:acetone (99.3:0.7% v/v) of 141 μL/well was dispensed into reactionassay blocks containing the substrate to obtain a final concentrationsof 70% IPA and 0.5% acetone in the reaction mixtures. Clear lysates of10 μL/well from lysate plates were transferred to the reaction mixtures.Plates were heat sealed and left to shake overnight at 50° C. and 575rpm.

Assay Protocol VI.

Cell pellets were processed as described in Assay Protocol_IV. Reactionconditions comprised oxcarbazepine, 75 g/L; NADP+, 0.05 g/L; IPA, 70%v/v; and lysate, 10 μL, 20 μL or 50 μL. Assays were carried out bydispensing 15-20 mg solid substrate into reaction assay blocks usingsolid dose template plate Millipore MACL09625, followed by 40 μL/well of0.25 g/L NADP+ prepared in 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0). IPA of140 μL/well was dispensed into reaction assay blocks. Clear lysates of20 μL/well from lysate plates were transferred to the reaction mixtures.Plates were heat sealed and left to shake at 57° C. and 575 rpm for thefollowing periods: (a) overnight, i.e., approximately 18 hrs, or (b) 4hrs.

Assay Protocol VII.

Cell pellets were processed as described in Assay Protocol_IV above.Reaction conditions comprised oxcarbazepine, 75 g/L; NADP⁺, 0.05 g/L;IPA/Acetone, 70:1% v/v; and lysate, 10 μL. Assays were carried out bydispensing 15-20 mg solid substrate into reaction assay blocks usingsolid dose template plate Millipore MACL09625, followed by 48 μL/well of0.21 g/L NADP⁺ prepared in 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0).IPA:acetone (98.6:1.4% v/v) of 142 μL/well were dispensed into reactionassay blocks containing substrate to obtain the final concentrations of70% IPA and 1% acetone in the reaction mixtures. Clear lysates of 10μL/well from lysate plates were respectively transferred to theirreaction mixtures. Plates were heat sealed and left to shake overnightat 57° C. with a speed of 575 rpm.

Assay Protocol VIII.

Oxcarbazepine, 75 g/L; NADP+, 0.05 g/L; IPA/Acetone, 70:1% v/v; andlysate, 10 μL. Assays were carried out by dispensing 15-20 mg solidsubstrate into reaction assay blocks using solid dose template plateMillipore MACL09625, followed by 48 μL/well of 0.21 g/L NADP+ preparedin 0.1M TEA-HCl with 1 mM MgSO₄ (pH 9.0). IPA:acetone (98.6:1.4% v/v) of142 μL/well was dispensed into reaction assay blocks containingsubstrate to obtain the final concentrations of 70% IPA and 1% acetonein the reaction mixtures. Clear lysates of 10 μL/well from lysate plateswere transferred to their reaction mixtures. Plates were heat sealed andleft to shake at 62° C. and 575 rpm for the following periods: (i)overnight i.e. approximately 18 hrs, or (ii) 6 hrs.

For reaction plates with substrate loaded as homogenous DMSO solution,after designated reaction times, plates were centrifuged at 4000 rpm for1 min at 25° C. Acetonitrile at 800 μL/well were added into the reactionassay mixes. Plates were heat sealed and vigorously shaken for about 15min at RT on titre-plate shaker (approximately 8 g) and visuallyinspected to ensure that there was no precipitation of substrates orproducts. Quenched plates were spun down at 4000 rpm for 10 min at 25°C.

For reaction plates with solid dosed substrate, after designatedreaction times, plates were centrifuged at 4000 rpm for 1 min at 25° C.DMSO of 1200 μL/well was added into the reaction assay mixes. Plateswere heat sealed and vigorously shaken for about 15 min at RT ontitre-plate shaker (approximately 8 g). Plates with quenched reactionswere visually inspected to ensure that all solid substrate weredissolved. When necessary, plates were shaken again for approximately 15min until no solid substrate was observed. Quenched reactions were leftto shake at 575 rpm for about 10 min at 45° C. to ensure that residualsolid substrate in the mixtures was dissolved. Quenched plates were spundown at 4000 rpm for 10 min at 25° C.

HPLC Screening Assay for Reactions with Solid Dosed Substrate.

HTP reaction assays performed using substrate loaded as DMSO solutionwere prepared for analysis by taking 40 μL of quenched reaction mixturesand diluting with 160 μL of acetonitrile in Costar™ 96-wells roundbottom plates.

HTP reaction assays performed using solid dosed substrate, i.e., highsubstrate loading of ˜75 g/L substrate was prepared for analysis bytaking 10 μL of quenched reaction mixtures and diluting with 190 μL ofacetonitrile in Costar™ 96-wells round bottom plates. The samples werethen analyzed by HPLC.

HPLC Protocol 1: HPLC chromatographic analysis used Agilent's EclipseXDB C-18 column, 4.6×150 mm, 5 μm diameter column, at a temperature of25° C., and a flowrate of 1.2 mL/min using a mobile phase of watercontaining 0.1% acetic acid/acetonitrile, 60/40% v/v, where the aceticacid is prepared in 18.2 MΩ cm−1 milli-Q™ water. The column detectionwavelengths were 210 nm, 230 nm and 254 nm. Retention time for theketone is ˜2.1 min, and retention time for the alcohol is ˜1.5 min,respectively. This protocol was primarily used for HTP screening assaysin all rounds.

HPLC Protocol 2: HPLC chromatographic analysis used Agilent's EclipseXDB C-8 column, 4.6×150 mm, 5 μm diameter column, at a temperature of25° C. and a flowrate of 1.5 mL/min using a mobile phase of 10 mMammonium acetate/acetonitrile, 45/55% v/v. The column detectionwavelengths were 210 nm, 230 nm and 254 nm. Retention time for theketone is ˜1.3 min and retention time for the alcohol is ˜1.1 min,respectively. This protocol was used for rapid screenings, e.g., inRound 1 libraries screenings.

Example 4 Biocatalytic Process I for Preparation of Compound (1c) fromCompound (2c)—25 g Scale Reaction

This example illustrates a first biocatalytic process using anengineered ketoreductase polypeptide of the disclosure to preparecompound (1c) on a 25 g scale. The reaction was carried out in anaqueous co-solvent system of 0.1 M TEA, 1 mM MgSO₄, pH 9.0, 70% IPA, andcompound (2a) loading of 50 g/L. The engineered ketoreductase (SEQ IDNO:36) was at a loading of 3 g/L along with co-factor NADPH at 0.1 g/L.The engineered ketoreductase also has secondary alcohol dehydrogenaseactivity, acting as a recycling system with the IPA to regenerate theoxidized co-factor NADP+ to NADPH through the oxidation of the IPA toacetone. Execution of this procedure as described afforded 23.2 g (93%isolated yield) of crude desired product in one run with 96.2% chemicalpurity (w/w, HPLC Method 5).

Reaction Protocol.

A 1 L baffled jacketed reactor was charged sequentially with thefollowing: 0.1 M TEA buffer solution (pH 9.0), 100 L; IPA, 350 mL;oxcarbazepine, 25 g charged as a solid. The reactor vessel was equippedwith an overhead anchor stirrer. A temperature probe was inserted tocheck the internal solution temperature and a nitrogen inlet connectedto a flow meter. An outlet tube with condenser was also attached. Thereaction mixture was stirred at 45° C. (internal temperature) at 200 rpmwith a nitrogen flow rate of 1 L/min for 10 min.

The reaction mixture was then charged sequentially with the following:NADP+ (50 mg), 1 mL prepared in TEA buffer; ketoreductase polypeptide ofSEQ ID NO: 36 (1.5 g of DSP Powder), and 10 mL prepared in TEA buffer.The reaction mixture at the start of the process is a white slurry withan initial pH of about 8. The reaction mixture was stirred at the aboveconditions for 24 hours. The reaction volume was maintained by theintermittent addition of deionized water (Total vol. added: 4×10 mL).After 8 hours, the nitrogen flow rate was turned off to prevent anysignificant overnight evaporation.

The reaction course was followed periodically by taking samples from thereaction mixture, quenching, and analyzing as described in Method 1.Samples were also frequently monitored for acetone content using theprocedure described in Method 4. For the purposes of tracking theprocess, t=0 was set at the time at which the enzyme was added.

After in-process analyses indicated >99% conversion (24 hours), thereaction mixture was taken for subsequent workup and isolation. Thesolution was allowed to cool to room temperature then drained from thereactor into a 500 mL round-bottom flask. IPA was distilled by rotaryevaporation (60 torr, 40° C. bath) until 5-10% IPA remained relative tothe start of distillation (IPA concentration determined by Method 4).

The crude product was collected by filtration through a sintered funneland washed with 20 mL of heptane. The solid was dried for 24 h undervacuum (3-20 mm Hg) at 30° C. Upon drying, 23.2 g (93% yield) of crudeproduct was obtained with a chemical purity of 96.2% (as determined byHPLC Method 5) and >99.9% e.e (as determined by HPLC Method 3). Theresidual protein content in the crude isolated product measured 0.87% byweight. The level of residual protein was measured using a UVabsorbance-based protein quantification assay (SPNTM-Assay) commerciallyavailable from G-Biosciences (Maryland Heights, Mo., USA).

Analytical Methods for Example 3.

Five different methods were used for determining % conversion, purity ofcompound (1a), enantiomeric purity, IPA and acetone concentration, and %potency.

Method 1—In-Process % Conversion.

To prepare a sample for HPLC analysis, 100 μL of reaction mixture wasquenched with 900 μL 1:1 DMSO:MeCN. The sample was centrifuged to removeprecipitated enzyme. 10 μL of supernatant was added to 990 μL MeCN andused for chromatographic analysis.

Method 1 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column Agilent Eclipse XDB C18 4.6 ×150 mm, 5 μm Mobile Phase MeCN/0.1% HOAc in water (40/60) Columntemperature 25° C. Flow rate 1.2 mL/min Injection volume 10 μL UVWavelength 210 nm Runtime 3.2 min Product 1.8 min Substrate 2.5 minLinearity 0.99 (R² at 2-200 ppm substrate and product) RF (Product tosubstrate) 1.23

The percent (%) conversion was calculated as follows:

${\%\mspace{14mu}{Conversion}} = {\frac{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{product}} \right\rbrack}{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{product}} \right\rbrack + \left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{substrate}*{RF}} \right\rbrack}*100\%}$

Method 2—Identification and Impurity Determination by HPLC.

20.0 mg of isolated eslicarbazepine was weighed into 100 mL volumetricflask and dissolved in approximately 80 mL in MeCN. The mixture wassonicated for 5 min and brought up to the final volume with MeCN.

Method 2 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column Agilent Eclipse XDB C18 4.6 ×150 mm, 5 μm Mobile Phase (Premixed) Gradient Eluent A: MeCN Eluent B:0.1% HOAc in water Time (min) Eluent A (%) Eluent B (%)  0 20 80 12 3070 18 50 50 20 50 50 22 20 80 Detection Wavelength 230 nm ColumnTemperature 25° C. Injection Volume 10 μL Run time 22 min (Post Time 8min) Product 6.2 min Substrate 10.7 min Flow rate 1 mL/min

Method 3—Enantiomeric Purity of (S)-licarbazepine.

Samples were prepared by taking 40.0 mg of isolated (S)-licarbazepineweighed into a 100 mL volumetric flask and dissolving in 80 mL of MeCN.The mixture was sonicated for 5 min and brought up to the final volumewith MeCN.

Method 3 Chromatographic Parameters

Instrument Agilent HPLC 1200 system Column Chiralcel OD-H, 4.6 × 250 mm,5 μm Mobile Phase (premixed) 90% n-Hexane, 10% IPA Flow Rate 2.0 mL/minDetection Wavelength 230 nm Column Temperature 15° C. Injection Volume10 μL Run time 35 min (R)-Eslicarbazepine 18.5 min (S)-Eslicarbazepine27.3 min

Enantiomeric purity was calculated as follows:

${\%\mspace{14mu}{e.e.}} = {\frac{\begin{matrix}{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}(S)\text{-}{licarbazepine}} \right\rbrack -} \\\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}(R)\text{-}{licarbazepine}} \right\rbrack\end{matrix}}{\begin{matrix}{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}(S)\text{-}{licarbazepine}} \right\rbrack +} \\\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}(R)\text{-}{licarbazepine}} \right\rbrack\end{matrix}} \times 100}$

Method 4—Determining Acetone and IPA Concentration (GC).

Samples for GC analysis were prepared by taking 100 μL of reactionsolution and adding it to 900 μL of methanol. Samples were centrifugedfor 1-2 min and 200 μL of supernatant dispensed into a GC glass vialwith insert.

Method 4 Chromatographic Parameters

Instrument Agilent GC 6890N Column Roticap WAX Capillary, 50 m × 250 μm(ID) × 0.25 μm (FT) Gas flow Helium with split ratio 60:1 Inlet Pressure22.4 psi Column Pressure 6.0 psi Helium flow rate 1.1 mL/min (ConstantPressure Mode) Inlet Temperature 180° C. Detector Temperature 200° C.FID Hydrogen Flow 30 mL/min FID Air Flow 350 mL/min FID Nitrogen Flow 35mL/min Injection Volume 1 μL Run time 6.71 min Acetone Retention Time3.97 min IPA Retention Time 4.41 min

Temperature Program:

Oven Ramp ° C./min Next ° C. Hold Time (min) Run Time (min) Initial 65 00 Ramp 7 105 1 6.71

Method 5—Determining (S)-licarbazepine % Potency.

Samples were prepared by placing 1.0 mg of reference standard into a 5mL volumetric flask and adding 4 mL MeCN to disperse the solid. Themixture was sonicated for 5 min, then made up to volume with MeCN. Afterpassing through a 0.5 μm disc membrane, a sample was injected into theHPLC using the chromatographic conditions specified below. Isolatedsample solution was prepared in the same way.

Method 5 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column Agilent Eclipse XDB C18 4.6 ×150 mm, 5 μm Mobile Phase (Premixed) MeCN/0.1% HOAc in water (25/75)Detection Wavelength 230 nm Column Temperature 25° C. Injection Volume10 μL Run time 10 min Flow rate 1.0 mL/min % Potency 96.2 LOD <0.2 ppm(S/N~3) LOQ <0.6 ppm (S/N~10)

Percent (%) potency was calculated as follows:

${\%\mspace{14mu}{potency}} = {\frac{{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{Sample} \times {Weight}\mspace{14mu}{of}\mspace{14mu}{Std} \times {Potency}\mspace{14mu}{of}\mspace{14mu}{Std}}{{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{Std} \times {Weight}\mspace{14mu}{of}\mspace{14mu}{Sample}} \times 100}$

Example 5 Biocatalytic Process I for Preparation of Compound (1c) fromCompound (2c)—50 g Scale Reaction

This example illustrates a second biocatalytic process using anengineered ketoreductase polypeptide to prepare compound (1c) on a 50 gscale. The reaction is carried out in an aqueous co-solvent system of0.1M TEA, 1 mM MgSO₄, pH 10, 60% IPA, and compound (2c) loading of 100g/L. The engineered ketoreductase (SEQ ID NO: 36) was at a loading of 1g/L along with co-factor NADPH at 0.1 g/L. This protocol afforded 48 g(96% isolated yield) of crude desired product in one run with 98.7%chemical purity (w/w, as determined by HPLC Method 5), >99.9%enantiomeric excess (as determined by HPLC Method 3) and a proteinresidue content of <100 ppm.

Biocatalytic Reaction Procedure.

A 1 L jacketed reactor was charged sequentially with the 300 mL of IPA,190 mL of TEA buffer solution (pH 10.0), and oxcarbazepine 50.0 g(charged as solid under stirring). The reaction vessel was equipped withan overhead stirrer fitted with an anchor shaped stir blade, atemperature probe, a nitrogen inlet connected to a flow meter and anoutlet for solvent collection. The reaction mixture was stirred at 200rpm and heated until an internal temperature of 55° C. was attained. Astock solution of enzyme and NADP, prepared separately in buffer, wascharged to the reaction mixture at 55° C. The reaction mixture wasstirred at 55° C., 200 rpm under a nitrogen atmosphere with a flow rateof 0.8 liters per minute. The reaction volume was maintained by theintermittent addition of a pre-mixed solution of 60% IPA and 40% buffer(0.1 M TEA with 1 mM MgSO₄, pH 10.0). The reaction course was followedperiodically by taking samples from the reaction mixture, quenching, andanalyzing as described in Method 1. Samples were also frequentlymonitored for acetone content using the procedure described in Method 4.For the purposes of tracking the process, t=0 was set at the time atwhich the enzyme was added. After in-process analyses indicated >99%conversion in 24 h, the reaction mixture was taken for subsequent workupand isolation.

Following complete conversion (>99%), the reaction mixture was drainedfrom the reactor into a 1 L round-bottom flask. IPA was distilled byrotary evaporation (75 torr, 50° C. bath). Upon partial distillation ofreaction volume, 100 mL of water was added to the white slurry and thedistillation continued to completely remove IPA.

The crude product was collected by filtration through a Buchner funneland washed with water (100 mL) and heptane (200 mL). The solid was driedfor 24 h in a vacuum oven (2 mbar) at 30° C. Upon drying, 48.0 g (96%yield) of crude product was obtained as an off white solid with achemical purity of 98.7% (as determined by HPLC Method 5) with >99.9%e.e (as determined by HPLC Method 3) and a residual protein content of80 ppm.

Purification of Compound (1c).

A 10 g suspension of crude product from above in 100 ml methanol washeated to 40° C. (internal temperature) to allow maximum dissolution ofproduct. Celite (2.0 g) was added to the slightly turbid solution, andthe mixture was stirred at 40° C. for 15-20 minutes. The slurry withCelite was then filtered through a sintered funnel, and the residue waswashed with 20 mL of pre-heated (˜40° C.) methanol. The clear filtrateobtained was then distilled under reduced pressure to reduce the volumeto approximately 30 mL. The thick solution was gradually cooled to 5° C.using an ice-bath. Cold water (50 mL) was added dropwise to the whiteprecipitate, and the resulting slurry was stirred at 5° C. for 30minutes. The precipitated product was filtered through a sinteredfunnel, rinsed and washed with 20 mL of water before being dried in avacuum oven for 16 h (30° C., 2 mbar). This resulted in 9.0 g (90%recovery) of purified product in a single run as a white solid with99.6% chemical purity (as determined by HPLC Method 5) and a residualprotein content of <10 ppm.

Analytical Methods Used in the Process of Example 4:

Chromatographic methods were employed to analyze the products of theketoreductase mediated conversion of compound (2c) to compound (1c)

Method 1—Rapid Conversion Method.

1 mL of reaction mixture was quenched in 9 mL of pre-mixed solution of1:1 DMSO:MeCN. The sample was sonicated to completely dissolve anyundissolved substrate or product. The sample was then centrifuged toseparate the enzyme from the solution. 50 μL of supernatant was added to950 μL MeCN and submitted for analysis.

Method 1 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column Agilent Eclipse XDB C18 4.6 ×150 mm, 5 μm Mobile Phase MeCN/0.1% AcOH in water (40/60, Isocratic)Column temperature 25° C. Flow rate 1.4 mL/min Injection volume 10 μL UVWavelength 210 nm Runtime 2.7 min Substrate 1.91 min Linearity 0.99 (R2at 2-200 ppm substrate and product) RF (product to substrate) 1.23

The % conversion was calculated from the chromatogram as follows:

${\%\mspace{14mu}{Conversion}} = {\frac{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{product}} \right\rbrack}{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{product}} \right\rbrack + \left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{substrate} \times {RF}} \right\rbrack} \times 100\%}$

Method 2—Purity Method (HPLC).

To Prepare The Sample For Analysis, 20.0 Mg Of Isolated eslicarbazepinewas weighed into 100 mL volumetric flask and dissolved in approximately80 mL in MeCN. The mixture was sonicated for 5 min and topped up tovolume with MeCN. Alternatively, the reaction sample prepared in Method1 above can also be used in this method to determine in-process purityand % conversion.

Method 2 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column Agilent Eclipse XDB C18 4.6 ×150 mm, 5 μm Mobile Phase (premixed) Gradient Eluent A: MeCN Eluent B:0.1% AcOH in water Time (min) Eluent A (%) Eluent B (%)  0 20 80 12 3070 18 50 50 20 50 50 22 20 80 Detection Wavelength 210 nm ColumnTemperature 25° C. Injection Volume 10 μL Run time 22 min Equilibrationtime 5 min Product 7.03 min Substrate 11.34 min Flow rate 1.0 mL/min

The % conversion was calculated by the same method described in Method 1above.

Method 3—Chiral Method (HPLC).

To prepare the sample, 40.0 mg of isolated S-licarbazepine was weighedinto a 100 mL volumetric flask and dissolved in 80 mL of MeCN. Themixture was sonicated for 5 min and topped up to volume with MeCN.

Method 3 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column ChiraDex ®, LiChroCART ®250-4, 5 μm Mobile Phase 95% Na₂HPO₄ (100 mM; pH 7.0) and 5% MeOH(premixed) Column temperature 15° C. Flow rate 1.0 mL/min Injectionvolume 10 μL Detection Wavelength 254 nm Runtime 24 min R-licarbazepine15.4 min S-licarbazepine 18.3 min

${\%\mspace{14mu}{e.e.}} = {\frac{\begin{matrix}{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu} S\text{-}{licarbazepine}} \right\rbrack -} \\\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu} R\text{-}{licarbazepine}} \right\rbrack\end{matrix}}{\begin{matrix}{\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu} S\text{-}{licarbazepine}} \right\rbrack +} \\\left\lbrack {{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu} R\text{-}{licarbazepine}} \right\rbrack\end{matrix}} \times 100}$

Method 4—Residual Solvent Detection Method (GC).

Sample was prepared by diluting 1 mL of reaction mixture with 9 mL ofmethanol, prior to centrifugation for 1 min. The supernatant was removedfor GC analysis.

Method 4 Chromatographic Parameters

Instrument Agilent GC 6890N Column Roticap WAX Capillary, 50 m × 250 μm(ID) × 0.25 μm (FT) Gas flow Helium with split ratio 60:1 Inlet Pressure22.4 psi Column Pressure 6.0 psi Helium flow rate 1.1 mL/min (ConstantPressure Mode) Inlet Temperature 180° C. Detector Temperature 200° C.FID Hydrogen Flow 30 mL/min FID Air Flow 350 mL/min FID Nitrogen Flow 35mL/min Injection Volume 1 μL Run time 6.7 min Acetone Retention Time 3.9min IPA Retention Time 4.4 minTemperature Program

Oven Ramp ° C./min Next ° C. Hold Time (min) Run Time (min) Initial 65 00 Ramp 7 105 1 6.71

Method 5—Potency Method (HPLC).

1.0 mg of reference standard eslicarbazepine was dissolved with 4 mLMeCN in a 5 mL volumetric flask. The solution was sonicated for 5 minand made up to volume with MeCN. After filtering the solution through a0.5 μm disc membrane, sample was used for HPLC analysis. Sample withisolated eslicarbazepine was prepared in a similar manner.

Method 5 Chromatographic Parameters

Instrument Agilent 1200 HPLC system Column Agilent Eclipse XDB C18 4.6 ×150 mm, 5 μm Mobile Phase (Premixed) MeCN/0.1% AcOH in water (25/75)Detection Wavelength 230 nm Column Temperature 25° C. Injection Volume10 μL Run time 10 min Flow rate 1.0 mL/min LOD <0.2 ppm (S/N~3) LOQ <0.6ppm (S/N~10)

% potency of isolated product is calculated as follows:

${\%\mspace{14mu}{potency}} = {\frac{\begin{matrix}{{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{Sample} \times} \\{{Weight}\mspace{14mu}{of}\mspace{14mu}{Standard} \times {Potency}\mspace{14mu}{of}\mspace{14mu}{Standard}}\end{matrix}}{{Peak}\mspace{14mu}{Area}\mspace{14mu}{of}\mspace{14mu}{Standard} \times {Weight}\mspace{14mu}{of}\mspace{14mu}{Sample}} \times 100}$

All publications, patents, patent applications and other documents citedin this application are hereby incorporated by reference in theirentireties for all purposes to the same extent as if each individualpublication, patent, patent application or other document wereindividually indicated to be incorporated by reference for all purposes.

While various specific embodiments have been illustrated and described,it will be appreciated that various changes can be made withoutdeparting from the spirit and scope of the invention(s).

What is claimed is:
 1. A process for preparing a compound of structuralformula (1) in enantiomeric excess,

wherein each ring A and B is independently an optionally substitutedmonocyclic aryl or heteroaryl, R¹ is selected from hydrogen, hydroxy,halo, cyano, carboxy, and an optionally substituted alkyl, aminoalkyl,cycloalkyl, heterocycloalkyl, alkyloxycarbonyl, aminocarbonyl,aminothiocarbonyl, aminosulfonyl, and sulfonyl; the process comprisingcontacting the compound of structural formula (2),

wherein A and B, and R¹ are defined above, with a ketoreductasepolypeptide comprising an amino acid sequence that has at least 80%sequence identity to the reference polypeptide of SEQ ID NO: 10, whereinthe amino acid sequence comprises X80 is T; X96 is V or R; X145 is L;X153 is T; X190 is P; X196 is L or M; and X226 is V, wherein theketoreductase is capable of converting compound (2) to compound (1) inenantiomeric excess, in presence of NADH or NADPH under suitablereaction conditions.
 2. The process of claim 1, wherein R¹ is selectedfrom H, —OH, —CN, —C(O)OR^(a), —(C1-C4)alkyl-NR^(b)R^(c),—C(O)NR^(b)R^(c), —C(S)NR^(b)R^(c), —SO₂NR^(b)R^(c), —SO₂R^(b),bicycloalkyl and heterobicycloalkyl, wherein R^(a), R^(b) and R^(c) areeach independently selected from H and an optionally substituted alkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl. 3.The process of claim 1, wherein the rings A and B are independently anoptionally substituted phenyl, pyridyl or thienyl.
 4. The process ofclaim 1, wherein the rings A and B are phenyl and R¹ is selected fromhydrogen, hydroxy, halo, cyano, carboxy, and an optionally substitutedalkyl, aminoalkyl, cycloalkyl, heterocycloalkyl, alkyloxycarbonyl,aminocarbonyl, aminothiocarbonyl, aminosulfonyl, and sulfonyl, andthereby forming a compound of structural formula (1a) in enantiomericexcess,


5. The process of claim 4, wherein R¹ is selected from H, —OH, —CN,—C(O)OR^(a), —(C1-C4)alkyl-NR^(b)R^(c), —C(O)NR^(b)R^(c),—C(S)NR^(b)R^(c), —SO₂NR^(b)R^(c), —SO₂R^(b), bicycloalkyl andheterobicycloalkyl, wherein R^(a), R^(b) and R^(c) are eachindependently selected from H and an optionally substituted alkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl. 6.The process of claim 4, wherein R¹ is selected from —OH, —C(O)OR^(d),—C(O)NH₂, —CN, dimethylaminopropyl, methylaminopropyl, andquinuclidinyl, wherein R^(d) is (C1-C4) alkyl.
 7. The process of claim6, wherein R¹ is —C(O)NH₂, thereby forming compound (1c) or a structuralanalog thereof in enantiomeric excess


8. The process of claim 1, wherein the amino acid sequence comprises atleast the following features: (a) X80 is T; X96 is V or R; X145 is L;X153 is T; X190 is P; X196 is L or M; and X226 is V; (b) X64 is V; X71is P; X80 is T; X87 is L; X94 is A or G; X96 is V; X145 is L; X147 is Qor M; X153 is T; X173 is L; X190 is P; X196 is M; X199 is M; and X226 isV; or (c) X17 is H or M; X25 is T; X29 is T; X40 is R; X43 is R or V;X64 is V; X71 is P or G; X80 is T; X87 is L; X94 is G; X95 is Y or M;X96 is R or V; X131 is C; X145 is L; X147 is Q or M; X152 is A or L;X153 is T; X157 is S; X173 is L; X190 is P; X196 is M or L; X199 is M;X200 is P; and X226 is V.
 9. The process of claim 7, wherein thereaction conditions comprise: (a) the ketoreductase polypeptide is atabout 1 g/L to about 10 g/L; (b) compound 2(c) or a structural analogthereof is at a loading concentration of about 50 g/L to about 175 g/L;(c) NADP(H) is about 0.5 g/L to about 1 g/L; (d) a co-solvent solutionof an aqueous buffer, and IPA of about 50 to about 70% (v/v), and (e) atemperature of about 45° C. to about 60° C.
 10. The process of claim 7,wherein compound (2c) or a structural analog thereof is at a loading ofabout 50 g/L to about 200 g/L and wherein the process results inenantiomeric excess of at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99% or greater of compound (1c) in 24 h or less.
 11. A method forpreparing compound of structural formula (6) in enantiomeric excess,

wherein R⁴ is selected from H, alkyl, aminoalkyl, haloalkyl, aralkyl,cycloalkyl, cycloalkylalkyl, alkoxy, aryl, substituted phenyl or pyridylgroup; the method comprising converting compound (2c) to compound (1c)in enantiomeric excess by the process of claim 7.